diff --git a/build.gradle b/build.gradle index 6e12edd5d..10447e69d 100644 --- a/build.gradle +++ b/build.gradle @@ -47,7 +47,7 @@ jacoco { toolVersion = "0.7.5.201505241946" } -final htsjdkVersion = System.getProperty('htsjdk.version', '2.10.0') +final htsjdkVersion = System.getProperty('htsjdk.version', '2.10.1') dependencies { compile 'com.google.guava:guava:15.0' diff --git a/src/main/java/picard/illumina/BasecallsConverter.java b/src/main/java/picard/illumina/BasecallsConverter.java new file mode 100644 index 000000000..c1ccf9f04 --- /dev/null +++ b/src/main/java/picard/illumina/BasecallsConverter.java @@ -0,0 +1,150 @@ +package picard.illumina; + +import htsjdk.samtools.util.Log; +import htsjdk.samtools.util.ProgressLogger; +import htsjdk.samtools.util.SortingCollection; +import picard.PicardException; +import picard.illumina.parser.ClusterData; +import picard.illumina.parser.IlluminaDataProviderFactory; +import picard.illumina.parser.readers.BclQualityEvaluationStrategy; + +import java.io.File; +import java.util.Comparator; +import java.util.List; +import java.util.Map; + +abstract class BasecallsConverter { + private static final Log log = Log.getInstance(BasecallsConverter.class); + + final Comparator outputRecordComparator; + final int maxReadsInRamPerTile; + final boolean demultiplex; + final List tmpDirs; + final boolean includeNonPfReads; + final boolean ignoreUnexpectedBarcodes; + final SortingCollection.Codec codecPrototype; + final Class outputRecordClass; + final Map> barcodeRecordWriterMap; + final ProgressLogger readProgressLogger = new ProgressLogger(log, 1000000, "Read"); + final ProgressLogger writeProgressLogger = new ProgressLogger(log, 1000000, "Write"); + int numThreads; + ClusterDataConverter converter = null; + + protected final BclQualityEvaluationStrategy bclQualityEvaluationStrategy; + protected List tiles; + protected final IlluminaDataProviderFactory factory; + + /** + * @param barcodeRecordWriterMap Map from barcode to CLUSTER_OUTPUT_RECORD writer. If demultiplex is false, must contain + * one writer stored with key=null. + * @param demultiplex If true, output is split by barcode, otherwise all are written to the same output stream. + * @param maxReadsInRamPerTile Configures number of reads each tile will store in RAM before spilling to disk. + * @param tmpDirs For SortingCollection spilling. + * @param numProcessors Controls number of threads. If <= 0, the number of threads allocated is + * available cores - numProcessors. + * @param outputRecordComparator For sorting output records within a single tile. + * @param codecPrototype For spilling output records to disk. + * @param outputRecordClass Inconveniently needed to create SortingCollections. + * @param includeNonPfReads If true, will include ALL reads (including those which do not have PF set) + * @param ignoreUnexpectedBarcodes If true, will ignore reads whose called barcode is not found in barcodeRecordWriterMap, + */ + BasecallsConverter(final Map> barcodeRecordWriterMap, + final int maxReadsInRamPerTile, + final List tmpDirs, + final SortingCollection.Codec codecPrototype, + final boolean ignoreUnexpectedBarcodes, + final boolean demultiplex, + final Comparator outputRecordComparator, + final boolean includeNonPfReads, + final BclQualityEvaluationStrategy bclQualityEvaluationStrategy, + final Class outputRecordClass, + final int numProcessors, + final IlluminaDataProviderFactory factory) { + + this.barcodeRecordWriterMap = barcodeRecordWriterMap; + this.maxReadsInRamPerTile = maxReadsInRamPerTile; + this.tmpDirs = tmpDirs; + this.codecPrototype = codecPrototype; + this.ignoreUnexpectedBarcodes = ignoreUnexpectedBarcodes; + this.demultiplex = demultiplex; + this.outputRecordComparator = outputRecordComparator; + this.includeNonPfReads = includeNonPfReads; + this.bclQualityEvaluationStrategy = bclQualityEvaluationStrategy; + this.outputRecordClass = outputRecordClass; + this.factory = factory; + + + if (numProcessors == 0) { + this.numThreads = Runtime.getRuntime().availableProcessors(); + } else if (numProcessors < 0) { + this.numThreads = Runtime.getRuntime().availableProcessors() + numProcessors; + } else { + this.numThreads = numProcessors; + } + } + + public IlluminaDataProviderFactory getFactory() { + return factory; + } + + public abstract void doTileProcessing(); + + /** + * Must be called before doTileProcessing. This is not passed in the ctor because often the + * IlluminaDataProviderFactory is needed in order to construct the converter. + * + * @param converter Converts ClusterData to CLUSTER_OUTPUT_RECORD + */ + void setConverter(final ClusterDataConverter converter) { + this.converter = converter; + } + + void setTileLimits(Integer firstTile, Integer tileLimit) { + if (firstTile != null) { + int i; + for (i = 0; i < tiles.size(); ++i) { + if (tiles.get(i).intValue() == firstTile.intValue()) { + tiles = tiles.subList(i, tiles.size()); + break; + } + } + if (tiles.get(0).intValue() != firstTile.intValue()) { + throw new PicardException("firstTile=" + firstTile + ", but that tile was not found."); + } + } + if (tileLimit != null && tiles.size() > tileLimit) { + tiles = tiles.subList(0, tileLimit); + } + } + + interface ClusterDataConverter { + /** + * Creates the OUTPUT_RECORDs from the cluster + */ + OUTPUT_RECORD convertClusterToOutputRecord(final ClusterData cluster); + } + + interface ConvertedClusterDataWriter { + void write(final OUTPUT_RECORD rec); + + void close(); + } + + /** + * A comparator for tile numbers, which are not necessarily ordered by the number's value. + */ + static final Comparator TILE_NUMBER_COMPARATOR = (integer1, integer2) -> { + final String s1 = integer1.toString(); + final String s2 = integer2.toString(); + // Because a the tile number is followed by a colon, a tile number that + // is a prefix of another tile number should sort after. (e.g. 10 sorts after 100). + if (s1.length() < s2.length()) { + if (s2.startsWith(s1)) { + return 1; + } + } else if (s2.length() < s1.length() && s1.startsWith(s2)) { + return -1; + } + return s1.compareTo(s2); + }; +} diff --git a/src/main/java/picard/illumina/CheckIlluminaDirectory.java b/src/main/java/picard/illumina/CheckIlluminaDirectory.java index 3f33dcd3b..068f9ee2e 100644 --- a/src/main/java/picard/illumina/CheckIlluminaDirectory.java +++ b/src/main/java/picard/illumina/CheckIlluminaDirectory.java @@ -8,22 +8,33 @@ import picard.cmdline.CommandLineProgram; import picard.cmdline.CommandLineProgramProperties; import picard.cmdline.Option; -import picard.cmdline.programgroups.Illumina; import picard.cmdline.StandardOptionDefinitions; +import picard.cmdline.programgroups.Illumina; import picard.illumina.parser.IlluminaDataProviderFactory; import picard.illumina.parser.IlluminaDataType; import picard.illumina.parser.IlluminaFileUtil; import picard.illumina.parser.OutputMapping; import picard.illumina.parser.ParameterizedFileUtil; import picard.illumina.parser.ReadStructure; +import picard.illumina.parser.readers.AbstractIlluminaPositionFileReader; +import picard.illumina.parser.readers.BaseBclReader; +import picard.illumina.parser.readers.CbclReader; +import picard.illumina.parser.readers.LocsFileReader; import java.io.File; import java.util.ArrayList; import java.util.Arrays; +import java.util.HashMap; import java.util.List; import java.util.Map; import java.util.Set; import java.util.TreeSet; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +import static picard.illumina.BasecallsConverter.TILE_NUMBER_COMPARATOR; +import static picard.illumina.NewIlluminaBasecallsConverter.getTiledFiles; +import static picard.illumina.parser.NewIlluminaDataProvider.fileToTile; /** * Program to check a lane of an Illumina output directory. This program checks that files exist, are non-zero in length, for every tile/cycle and @@ -40,7 +51,7 @@ "and are reasonably sized for every tile and cycle. Reasonably sized means non-zero sized for files that exist per tile and " + "equal size for binary files that exist per cycle or per tile. If DATA_TYPES {Position, BaseCalls, QualityScores, PF," + " or Barcodes} are not specified, then the default data types used by IlluminaBasecallsToSam are used. " + - "CheckIlluminaDirectory DOES NOT check that the individual records in a file are well-formed.

" + + "CheckIlluminaDirectory DOES NOT check that the individual records in a file are well-formed.

" + "" + "

Usage example:

" + "
" +
@@ -50,8 +61,7 @@
             "      LANES=1 \\
" +
             "      DATA_TYPES=BaseCalls " +
             "
" + - "
" - ; + "
"; private static final Log log = Log.getInstance(CheckIlluminaDirectory.class); // The following attributes define the command-line arguments @@ -90,6 +100,9 @@ optional = true) public Boolean LINK_LOCS = false; + @Option(doc = "Use the new converter. Defaults to false", optional = true) + public boolean USE_NEW_CONVERTER = false; + /** * Required main method implementation. */ @@ -113,30 +126,86 @@ protected int doWork() { log.info("Expected cycles: " + StringUtil.intValuesToString(expectedCycles)); for (final Integer lane : LANES) { - IlluminaFileUtil fileUtil = new IlluminaFileUtil(BASECALLS_DIR, lane); - final List expectedTiles = fileUtil.getExpectedTiles(); - if (!TILE_NUMBERS.isEmpty()) { - expectedTiles.retainAll(TILE_NUMBERS); - } + if (USE_NEW_CONVERTER) { + List tiles = new ArrayList<>(); + + File laneDir = new File(BASECALLS_DIR, IlluminaFileUtil.longLaneStr(lane)); + + File[] cycleDirs = IOUtil.getFilesMatchingRegexp(laneDir, IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN); + + //check all bcls/cbcls + List cbcls = new ArrayList<>(); + Arrays.asList(cycleDirs) + .forEach(cycleDir -> cbcls.addAll( + Arrays.asList(IOUtil.getFilesMatchingRegexp( + cycleDir, "^" + IlluminaFileUtil.longLaneStr(lane) + "_(\\d{1,5}).cbcl$")))); + IOUtil.assertFilesAreReadable(cbcls); + + //check all pf filter files + Pattern laneTileRegex = Pattern.compile(ParameterizedFileUtil.escapePeriods( + ParameterizedFileUtil.makeLaneTileRegex(".filter", lane))); + File[] filterFiles = getTiledFiles(laneDir, laneTileRegex); + for (File filterFile : filterFiles) { + Matcher tileMatcher = laneTileRegex.matcher(filterFile.getName()); + if (tileMatcher.matches()) { + tiles.add(Integer.valueOf(tileMatcher.group(1))); + } + } + IOUtil.assertFilesAreReadable(Arrays.asList(filterFiles)); + tiles.sort(TILE_NUMBER_COMPARATOR); + + //check s.locs + File locsFile = new File(BASECALLS_DIR.getParentFile(), "s.locs"); + LocsFileReader locsFileReader = new LocsFileReader(locsFile); + List locs = new ArrayList<>(); + while (locsFileReader.hasNext()) { + locs.add(locsFileReader.next()); + } - if (LINK_LOCS) { - createLocFileSymlinks(fileUtil, lane); - //we need to create a new file util because it stores a cache to the files it found on - //construction and this doesn't inclue the recently created symlinks - fileUtil = new IlluminaFileUtil(BASECALLS_DIR, lane); - } + Map filterFileMap = new HashMap<>(); + for (File filterFile : filterFiles) { + filterFileMap.put(fileToTile(filterFile.getName()), filterFile); + } - log.info("Checking lane " + lane); - log.info("Expected tiles: " + StringUtil.join(", ", expectedTiles)); + CbclReader reader = new CbclReader(cbcls, filterFileMap, readStructure.readLengths, tiles.get(0), locs, true); - final int numFailures = verifyLane(fileUtil, expectedTiles, expectedCycles, DATA_TYPES, FAKE_FILES); + reader.getAllTiles().forEach((key, value) -> { + List fileForCycle = reader.getFilesForCycle(key); + final long totalFilesSize = fileForCycle.stream().mapToLong(file -> file.length() - reader.getHeaderSize()).sum(); + final long expectedFileSize = value.stream().mapToLong(BaseBclReader.TileData::getCompressedBlockSize).sum(); + + if (expectedFileSize != totalFilesSize) { + throw new PicardException(String.format("File %s is not the expected size of %d instead it is %d", + fileForCycle, expectedFileSize, totalFilesSize)); + } + }); - if (numFailures > 0) { - log.info("Lane " + lane + " FAILED " + " Total Errors: " + numFailures); - failingLanes.add(lane); - totalFailures += numFailures; } else { - log.info("Lane " + lane + " SUCCEEDED "); + IlluminaFileUtil fileUtil = new IlluminaFileUtil(BASECALLS_DIR, lane); + final List expectedTiles = fileUtil.getExpectedTiles(); + if (!TILE_NUMBERS.isEmpty()) { + expectedTiles.retainAll(TILE_NUMBERS); + } + + if (LINK_LOCS) { + createLocFileSymlinks(fileUtil, lane); + //we need to create a new file util because it stores a cache to the files it found on + //construction and this doesn't inclue the recently created symlinks + fileUtil = new IlluminaFileUtil(BASECALLS_DIR, lane); + } + + log.info("Checking lane " + lane); + log.info("Expected tiles: " + StringUtil.join(", ", expectedTiles)); + + final int numFailures = verifyLane(fileUtil, expectedTiles, expectedCycles, DATA_TYPES, FAKE_FILES); + + if (numFailures > 0) { + log.info("Lane " + lane + " FAILED " + " Total Errors: " + numFailures); + failingLanes.add(lane); + totalFailures += numFailures; + } else { + log.info("Lane " + lane + " SUCCEEDED "); + } } } diff --git a/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java b/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java index 257281871..74e856626 100644 --- a/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java +++ b/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java @@ -24,21 +24,26 @@ package picard.illumina; +import htsjdk.samtools.metrics.MetricsFile; +import htsjdk.samtools.util.Histogram; +import htsjdk.samtools.util.IOUtil; +import htsjdk.samtools.util.StringUtil; import picard.PicardException; import picard.cmdline.CommandLineProgram; import picard.cmdline.CommandLineProgramProperties; -import picard.cmdline.programgroups.Illumina; import picard.cmdline.Option; import picard.cmdline.StandardOptionDefinitions; -import picard.illumina.parser.ClusterData;import picard.illumina.parser.IlluminaDataProvider;import picard.illumina.parser.IlluminaDataProviderFactory;import picard.illumina.parser.IlluminaDataType;import picard.illumina.parser.ReadStructure;import picard.illumina.parser.readers.BclQualityEvaluationStrategy; -import htsjdk.samtools.util.IOUtil; -import htsjdk.samtools.metrics.MetricsFile; -import htsjdk.samtools.util.Histogram; +import picard.cmdline.programgroups.Illumina; +import picard.illumina.parser.BaseIlluminaDataProvider; +import picard.illumina.parser.ClusterData; +import picard.illumina.parser.IlluminaDataProviderFactory; +import picard.illumina.parser.IlluminaDataType; +import picard.illumina.parser.ReadStructure; +import picard.illumina.parser.readers.BclQualityEvaluationStrategy; import picard.util.TabbedTextFileWithHeaderParser; -import htsjdk.samtools.util.StringUtil; import java.io.File; -import java.lang.Comparable;import java.lang.Double;import java.lang.Exception;import java.lang.Integer;import java.lang.Math;import java.lang.Override;import java.lang.String;import java.lang.StringBuilder;import java.text.DecimalFormat; +import java.text.DecimalFormat; import java.util.SortedMap; import java.util.TreeMap; @@ -178,7 +183,7 @@ protected int doWork() { unmatched_barcode = StringUtil.repeatCharNTimes('N', barcodeLength); //Initialize data provider, iterate over clusters, and collect statistics - final IlluminaDataProvider provider = factory.makeDataProvider(); + final BaseIlluminaDataProvider provider = factory.makeDataProvider(); while (provider.hasNext()) { final ClusterData cluster = provider.next(); diff --git a/src/main/java/picard/illumina/CollectIlluminaLaneMetrics.java b/src/main/java/picard/illumina/CollectIlluminaLaneMetrics.java index fdbd4f8d7..4d4c60bbc 100644 --- a/src/main/java/picard/illumina/CollectIlluminaLaneMetrics.java +++ b/src/main/java/picard/illumina/CollectIlluminaLaneMetrics.java @@ -39,15 +39,21 @@ import picard.cmdline.Option; import picard.cmdline.StandardOptionDefinitions; import picard.cmdline.programgroups.Illumina; -import picard.illumina.parser.*; +import picard.illumina.parser.ReadDescriptor; +import picard.illumina.parser.ReadStructure; +import picard.illumina.parser.ReadType; +import picard.illumina.parser.Tile; +import picard.illumina.parser.TileMetricsUtil; +import javax.xml.parsers.DocumentBuilderFactory; import java.io.File; import java.io.FileNotFoundException; -import java.util.*; +import java.util.ArrayList; +import java.util.Collection; +import java.util.List; +import java.util.Map; import java.util.stream.Collectors; -import javax.xml.parsers.DocumentBuilderFactory; - /** * Command-line wrapper around {@link IlluminaLaneMetricsCollector}. * @author mccowan @@ -92,6 +98,9 @@ @Option(shortName = "EXT", doc="Append the given file extension to all metric file names (ex. OUTPUT.illumina_lane_metrics.EXT). None if null", optional=true) public String FILE_EXTENSION = null; + @Option(doc = "Boolean the determines if this run is a NovaSeq run or not. (NovaSeq tile metrics files are in cycle 25 directory.", optional = true) + public boolean IS_NOVASEQ = false; + @Override protected int doWork() { final MetricsFile> laneMetricsFile = this.getMetricsFile(); @@ -119,7 +128,9 @@ protected int doWork() { } } - IlluminaLaneMetricsCollector.collectLaneMetrics(RUN_DIRECTORY, OUTPUT_DIRECTORY, OUTPUT_PREFIX, laneMetricsFile, phasingMetricsFile, READ_STRUCTURE, FILE_EXTENSION == null ? "" : FILE_EXTENSION, VALIDATION_STRINGENCY); + IlluminaLaneMetricsCollector.collectLaneMetrics(RUN_DIRECTORY, OUTPUT_DIRECTORY, OUTPUT_PREFIX, + laneMetricsFile, phasingMetricsFile, + READ_STRUCTURE, FILE_EXTENSION == null ? "" : FILE_EXTENSION, VALIDATION_STRINGENCY, IS_NOVASEQ); return 0; } @@ -135,18 +146,30 @@ public static void main(final String[] args) { private final static Log LOG = Log.getInstance(IlluminaLaneMetricsCollector.class); /** Returns a partitioned collection of lane number to Tile objects from the provided basecall directory. */ - public static Map> readLaneTiles(final File illuminaRunDirectory, final ReadStructure readStructure, final ValidationStringency validationStringency) { + public static Map> readLaneTiles(final File illuminaRunDirectory, + final ReadStructure readStructure, + final ValidationStringency validationStringency, + final boolean isNovaSeq) { final Collection tiles; try { - tiles = TileMetricsUtil.parseTileMetrics(TileMetricsUtil.renderTileMetricsFileFromBasecallingDirectory(illuminaRunDirectory), - readStructure, - validationStringency - ); + File tileMetricsOutFile = TileMetricsUtil.renderTileMetricsFileFromBasecallingDirectory(illuminaRunDirectory, isNovaSeq); + if (isNovaSeq) { + tiles = TileMetricsUtil.parseTileMetrics( + tileMetricsOutFile, + TileMetricsUtil.renderPhasingMetricsFilesFromBasecallingDirectory(illuminaRunDirectory), + readStructure, + validationStringency); + } else { + tiles = TileMetricsUtil.parseTileMetrics(tileMetricsOutFile, + readStructure, + validationStringency + ); + } } catch (final FileNotFoundException e) { throw new PicardException("Unable to open laneMetrics file.", e); } - return tiles.stream().collect(Collectors.groupingBy(Tile::getLaneNumber)); + return tiles.stream().filter(tile -> tile.getLaneNumber() > 0).collect(Collectors.groupingBy(Tile::getLaneNumber)); } /** Parses the tile data from the basecall directory and writes to both the lane and phasing metrics files */ @@ -154,17 +177,18 @@ public static void collectLaneMetrics(final File runDirectory, final File output final MetricsFile> laneMetricsFile, final MetricsFile> phasingMetricsFile, final ReadStructure readStructure, final String fileExtension, - final ValidationStringency validationStringency) { - final Map> laneTiles = readLaneTiles(runDirectory, readStructure, validationStringency); + final ValidationStringency validationStringency, + final boolean isNovaSeq) { + final Map> laneTiles = readLaneTiles(runDirectory, readStructure, validationStringency, isNovaSeq); writeLaneMetrics(laneTiles, outputDirectory, outputPrefix, laneMetricsFile, fileExtension); - writePhasingMetrics(laneTiles, outputDirectory, outputPrefix, phasingMetricsFile, fileExtension); + writePhasingMetrics(laneTiles, outputDirectory, outputPrefix, phasingMetricsFile, fileExtension, isNovaSeq); } public static File writePhasingMetrics(final Map> laneTiles, final File outputDirectory, final String outputPrefix, final MetricsFile> phasingMetricsFile, - final String fileExtension) { + final String fileExtension, boolean isNovaSeq) { laneTiles.entrySet().stream().forEach(entry -> IlluminaPhasingMetrics.getPhasingMetricsForTiles(entry.getKey().longValue(), - entry.getValue()).forEach(phasingMetricsFile::addMetric)); + entry.getValue(), !isNovaSeq).forEach(phasingMetricsFile::addMetric)); return writeMetrics(phasingMetricsFile, outputDirectory, outputPrefix, IlluminaPhasingMetrics.getExtension() + fileExtension); } diff --git a/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java b/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java index fd434ad5f..0016bc277 100644 --- a/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java +++ b/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java @@ -32,10 +32,10 @@ import picard.cmdline.CommandLineProgram; import picard.cmdline.CommandLineProgramProperties; import picard.cmdline.Option; -import picard.cmdline.programgroups.Illumina; import picard.cmdline.StandardOptionDefinitions; +import picard.cmdline.programgroups.Illumina; +import picard.illumina.parser.BaseIlluminaDataProvider; import picard.illumina.parser.ClusterData; -import picard.illumina.parser.IlluminaDataProvider; import picard.illumina.parser.IlluminaDataProviderFactory; import picard.illumina.parser.IlluminaDataType; import picard.illumina.parser.ReadDescriptor; @@ -109,21 +109,20 @@ "

For poorly matching barcodes, the order of specification of barcodes can cause arbitrary output differences.

" + "" + "

Usage example:

" + - "
" +
-                "java -jar picard.jar ExtractIlluminaBarcodes \\
" +
-        "              BASECALLS_DIR=/BaseCalls/ \\
" +
-        "              LANE=1 \\
" +
+            "
" +
+            "java -jar picard.jar ExtractIlluminaBarcodes \\
" +
+            "              BASECALLS_DIR=/BaseCalls/ \\
" +
+            "              LANE=1 \\
" +
             "          READ_STRUCTURE=25T8B25T \\
" +
-        "              BARCODE_FILE=barcodes.txt \\
" +
-        "              METRICS_FILE=metrics_output.txt " +
+            "              BARCODE_FILE=barcodes.txt \\
" +
+            "              METRICS_FILE=metrics_output.txt " +
             "
" +
             "" +
             "Please see the ExtractIlluminaBarcodes.BarcodeMetric " +
             "definitions " +
             "for a complete description of the metrics produced by this tool.
" +
             "" +
-            "
"
-    ;
+            "
";
 
     // The following attributes define the command-line arguments
 
@@ -177,7 +176,9 @@
 
     private static final Log LOG = Log.getInstance(ExtractIlluminaBarcodes.class);
 
-    /** The read structure of the actual Illumina Run, i.e. the readStructure of the input data */
+    /**
+     * The read structure of the actual Illumina Run, i.e. the readStructure of the input data
+     */
     private ReadStructure readStructure;
 
     private IlluminaDataProviderFactory factory;
@@ -242,7 +243,7 @@ protected int doWork() {
         }
         try {
             for (final PerTileBarcodeExtractor extractor : extractors) {
-                pool.submit(extractor);    
+                pool.submit(extractor);
             }
             pool.shutdown();
             // Wait a while for existing tasks to terminate
@@ -349,7 +350,9 @@ public static void finalizeMetrics(final Map barcodeToMet
         }
     }
 
-    /** Create a barcode filename corresponding to the given tile qseq file. */
+    /**
+     * Create a barcode filename corresponding to the given tile qseq file.
+     */
     private File getBarcodeFile(final int tile) {
         return new File(OUTPUT_DIR,
                 "s_" + LANE + "_" + tileNumberFormatter.format(tile) + "_barcode.txt" + (COMPRESS_OUTPUTS ? ".gz" : ""));
@@ -359,7 +362,7 @@ private File getBarcodeFile(final int tile) {
      * Validate that POSITION >= 1, and that all BARCODEs are the same length and unique
      *
      * @return null if command line is valid.  If command line is invalid, returns an array of error message
-     *         to be written to the appropriate place.
+     * to be written to the appropriate place.
      */
     @Override
     protected String[] customCommandLineValidation() {
@@ -456,23 +459,41 @@ private void parseBarcodeFile(final ArrayList messages) {
          * do not match a barcode.
          */
         public String BARCODE;
-        /** The barcode name. */
+        /**
+         * The barcode name.
+         */
         public String BARCODE_NAME = "";
-        /** The name of the library */
+        /**
+         * The name of the library
+         */
         public String LIBRARY_NAME = "";
-        /** The total number of reads matching the barcode. */
+        /**
+         * The total number of reads matching the barcode.
+         */
         public int READS = 0;
-        /** The number of PF reads matching this barcode (always less than or equal to READS). */
+        /**
+         * The number of PF reads matching this barcode (always less than or equal to READS).
+         */
         public int PF_READS = 0;
-        /** The number of all reads matching this barcode that matched with 0 errors or no-calls. */
+        /**
+         * The number of all reads matching this barcode that matched with 0 errors or no-calls.
+         */
         public int PERFECT_MATCHES = 0;
-        /** The number of PF reads matching this barcode that matched with 0 errors or no-calls. */
+        /**
+         * The number of PF reads matching this barcode that matched with 0 errors or no-calls.
+         */
         public int PF_PERFECT_MATCHES = 0;
-        /** The number of all reads matching this barcode that matched with 1 error or no-call. */
+        /**
+         * The number of all reads matching this barcode that matched with 1 error or no-call.
+         */
         public int ONE_MISMATCH_MATCHES = 0;
-        /** The number of PF reads matching this barcode that matched with 1 error or no-call. */
+        /**
+         * The number of PF reads matching this barcode that matched with 1 error or no-call.
+         */
         public int PF_ONE_MISMATCH_MATCHES = 0;
-        /** The fraction of all reads in the lane that matched to this barcode. */
+        /**
+         * The fraction of all reads in the lane that matched to this barcode.
+         */
         public double PCT_MATCHES = 0d;
         /**
          * The rate of all reads matching this barcode to all reads matching the most prevelant barcode. For the
@@ -482,7 +503,9 @@ private void parseBarcodeFile(final ArrayList messages) {
          * in representation between barcodes.
          */
         public double RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT = 0d;
-        /** The fraction of PF reads in the lane that matched to this barcode. */
+        /**
+         * The fraction of PF reads in the lane that matched to this barcode.
+         */
         public double PF_PCT_MATCHES = 0d;
 
         /**
@@ -515,12 +538,16 @@ public BarcodeMetric(final String barcodeName, final String libraryName,
             }
         }
 
-        /** This ctor is necessary for when reading metrics from file */
+        /**
+         * This ctor is necessary for when reading metrics from file
+         */
         public BarcodeMetric() {
             barcodeBytes = null;
         }
 
-        /** Creates a copy of metric initialized with only non-accumulated and non-calculated values set */
+        /**
+         * Creates a copy of metric initialized with only non-accumulated and non-calculated values set
+         */
         public static BarcodeMetric copy(final BarcodeMetric metric) {
             final BarcodeMetric result = new BarcodeMetric();
             result.BARCODE = metric.BARCODE;
@@ -546,24 +573,36 @@ public void merge(final BarcodeMetric metric) {
 
     }
 
-    /** Extracts barcodes and accumulates metrics for an entire tile. */
-    private static class PerTileBarcodeExtractor implements Runnable {
+    /**
+     * Extracts barcodes and accumulates metrics for an entire tile.
+     */
+    public static class PerTileBarcodeExtractor implements Runnable {
         private final int tile;
         private final File barcodeFile;
         private final Map metrics;
         private final BarcodeMetric noMatch;
         private Exception exception = null;
         private final boolean usingQualityScores;
-        private final IlluminaDataProvider provider;
+        private final BaseIlluminaDataProvider provider;
         private final ReadStructure outputReadStructure;
         private final int maxNoCalls, maxMismatches, minMismatchDelta, minimumBaseQuality;
 
-        /** Utility class to hang onto data about the best match for a given barcode */
-        class BarcodeMatch {
+        /**
+         * Utility class to hang onto data about the best match for a given barcode
+         */
+        public static class BarcodeMatch {
             boolean matched;
             String barcode;
             int mismatches;
             int mismatchesToSecondBest;
+
+            public boolean isMatched() {
+                return matched;
+            }
+
+            public String getBarcode() {
+                return barcode;
+            }
         }
 
         /**
@@ -607,11 +646,17 @@ public PerTileBarcodeExtractor(
             return this.metrics;
         }
 
-        public synchronized BarcodeMetric getNoMatchMetric() { return this.noMatch; }
+        public synchronized BarcodeMetric getNoMatchMetric() {
+            return this.noMatch;
+        }
 
-        public synchronized Exception getException() { return this.exception; }
+        public synchronized Exception getException() {
+            return this.exception;
+        }
 
-        /** run method which extracts barcodes and accumulates metrics for an entire tile */
+        /**
+         * run method which extracts barcodes and accumulates metrics for an entire tile
+         */
         synchronized public void run() {
             try {
                 LOG.info("Extracting barcodes for tile " + tile);
@@ -634,7 +679,9 @@ synchronized public void run() {
                         if (usingQualityScores) qualityScores[i] = cluster.getRead(barcodeIndices[i]).getQualities();
                     }
                     final boolean passingFilter = cluster.isPf();
-                    final BarcodeMatch match = findBestBarcodeAndUpdateMetrics(barcodeSubsequences, qualityScores, passingFilter, metrics, noMatch);
+                    final BarcodeMatch match = findBestBarcodeAndUpdateMetrics(barcodeSubsequences, qualityScores,
+                            passingFilter, metrics, noMatch, maxNoCalls, maxMismatches,
+                            minMismatchDelta, minimumBaseQuality);
 
                     final String yOrN = (match.matched ? "Y" : "N");
 
@@ -649,8 +696,7 @@ synchronized public void run() {
             } catch (final Exception e) {
                 LOG.error(e, "Error processing tile ", this.tile);
                 this.exception = e;
-            }
-            finally{
+            } finally {
                 provider.close();
             }
         }
@@ -662,11 +708,15 @@ synchronized public void run() {
          * @param passingFilter    PF flag for the current read
          * @return perfect barcode string, if there was a match within tolerance, or null if not.
          */
-        private BarcodeMatch findBestBarcodeAndUpdateMetrics(final byte[][] readSubsequences,
-                                                             final byte[][] qualityScores,
-                                                             final boolean passingFilter,
-                                                             final Map metrics,
-                                                             final BarcodeMetric noMatchBarcodeMetric) {
+        public static BarcodeMatch findBestBarcodeAndUpdateMetrics(final byte[][] readSubsequences,
+                                                                   final byte[][] qualityScores,
+                                                                   final boolean passingFilter,
+                                                                   final Map metrics,
+                                                                   final BarcodeMetric noMatchBarcodeMetric,
+                                                                   final int maxNoCalls,
+                                                                   final int maxMismatches,
+                                                                   final int minMismatchDelta,
+                                                                   final int minimumBaseQuality) {
             BarcodeMetric bestBarcodeMetric = null;
             int totalBarcodeReadBases = 0;
             int numNoCalls = 0; // NoCalls are calculated for all the barcodes combined
@@ -682,7 +732,7 @@ private BarcodeMatch findBestBarcodeAndUpdateMetrics(final byte[][] readSubseque
             int numMismatchesInSecondBestBarcode = totalBarcodeReadBases + 1;
 
             for (final BarcodeMetric barcodeMetric : metrics.values()) {
-                final int numMismatches = countMismatches(barcodeMetric.barcodeBytes, readSubsequences, qualityScores);
+                final int numMismatches = countMismatches(barcodeMetric.barcodeBytes, readSubsequences, qualityScores, minimumBaseQuality);
                 if (numMismatches < numMismatchesInBestBarcode) {
                     if (bestBarcodeMetric != null) {
                         numMismatchesInSecondBestBarcode = numMismatchesInBestBarcode;
@@ -746,7 +796,7 @@ private BarcodeMatch findBestBarcodeAndUpdateMetrics(final byte[][] readSubseque
          *
          * @return how many bases did not match
          */
-        private int countMismatches(final byte[][] barcodeBytes, final byte[][] readSubsequence, final byte[][] qualities) {
+        private static int countMismatches(final byte[][] barcodeBytes, final byte[][] readSubsequence, final byte[][] qualities, int minimumBaseQuality) {
             int numMismatches = 0;
             // Read sequence and barcode length may not be equal, so we just use the shorter of the two
             for (int j = 0; j < barcodeBytes.length; j++) {
diff --git a/src/main/java/picard/illumina/IlluminaBasecallsConverter.java b/src/main/java/picard/illumina/IlluminaBasecallsConverter.java
index 2be747f28..bdb650c74 100644
--- a/src/main/java/picard/illumina/IlluminaBasecallsConverter.java
+++ b/src/main/java/picard/illumina/IlluminaBasecallsConverter.java
@@ -25,11 +25,10 @@
 
 import htsjdk.samtools.util.Log;
 import htsjdk.samtools.util.PeekIterator;
-import htsjdk.samtools.util.ProgressLogger;
 import htsjdk.samtools.util.SortingCollection;
 import picard.PicardException;
+import picard.illumina.parser.BaseIlluminaDataProvider;
 import picard.illumina.parser.ClusterData;
-import picard.illumina.parser.IlluminaDataProvider;
 import picard.illumina.parser.IlluminaDataProviderFactory;
 import picard.illumina.parser.IlluminaDataType;
 import picard.illumina.parser.ReadStructure;
@@ -61,12 +60,12 @@
 
 /**
  * Manages the conversion of Illumina basecalls into some output format.  Creates multiple threads to manage reading,
- * sorting and writing efficiently.  Output is written in queryname output.  Optionally demultiplexes indexed reads
+ * sorting and writing efficiently.  Output is written in query name output.  Optionally demultiplexes indexed reads
  * into separate outputs by barcode.
  *
  * @param  The class to which a ClusterData is converted in preparation for writing.
  */
-public class IlluminaBasecallsConverter {
+public class IlluminaBasecallsConverter extends BasecallsConverter {
     /**
      * Describes the state of a barcode's data's processing in the context of a tile.  It is either not available in
      * that tile, has been read, has been queued to be written to file, or has been written to file.  A barcode only
@@ -93,115 +92,75 @@
         DATA_TYPES_WITH_BARCODE[DATA_TYPES_WITH_BARCODE.length - 1] = IlluminaDataType.Barcodes;
     }
 
-    /**
-     * A comparator for tile numbers, which are not necessarily ordered by the number's value.
-     */
-    public static final Comparator TILE_NUMBER_COMPARATOR = new Comparator() {
-        @Override
-        public int compare(final Integer integer1, final Integer integer2) {
-            final String s1 = integer1.toString();
-            final String s2 = integer2.toString();
-            // Because a the tile number is followed by a colon, a tile number that
-            // is a prefix of another tile number should sort after. (e.g. 10 sorts after 100).
-            if (s1.length() < s2.length()) {
-                if (s2.startsWith(s1)) {
-                    return 1;
-                }
-            } else if (s2.length() < s1.length() && s1.startsWith(s2)) {
-                return -1;
-            }
-            return s1.compareTo(s2);
-        }
-    };
-
-    private final Comparator outputRecordComparator;
-
-    private final BclQualityEvaluationStrategy bclQualityEvaluationStrategy;
-    private final Map> barcodeRecordWriterMap;
-    private final int maxReadsInRamPerTile;
-    private final boolean demultiplex;
-    private final List tmpDirs;
-    private final IlluminaDataProviderFactory factory;
-    private ClusterDataConverter converter = null;
-    private final ProgressLogger readProgressLogger = new ProgressLogger(log, 1000000, "Read");
-    private final ProgressLogger writeProgressLogger = new ProgressLogger(log, 1000000, "Write");
-    private int numThreads;
     // If FORCE_GC, this is non-null.  For production this is not necessary because it will run until the JVM
     // ends, but for unit testing it is desirable to stop the task when done with this instance.
     private final TimerTask gcTimerTask;
-    private List tiles;
-    private final boolean includeNonPfReads;
-    private final boolean ignoreUnexpectedBarcodes;
-
-    private final SortingCollection.Codec codecPrototype;
-    // Annoying that we need this.
-    private final Class outputRecordClass;
 
     /**
-	 * @param basecallsDir           Where to read basecalls from.
-	 * @param lane                   What lane to process.
-	 * @param readStructure          How to interpret each cluster.
-	 * @param barcodeRecordWriterMap Map from barcode to CLUSTER_OUTPUT_RECORD writer.  If demultiplex is false, must contain
-	 *                               one writer stored with key=null.
-	 * @param demultiplex            If true, output is split by barcode, otherwise all are written to the same output stream.
-	 * @param maxReadsInRamPerTile   Configures number of reads each tile will store in RAM before spilling to disk.
-	 * @param tmpDirs                For SortingCollection spilling.
-	 * @param numProcessors          Controls number of threads.  If <= 0, the number of threads allocated is
-	 *                               available cores - numProcessors.
-	 * @param forceGc                Force explicit GC periodically.  This is good for causing memory maps to be released.
-	 * @param firstTile              (For debugging) If non-null, start processing at this tile.
-	 * @param tileLimit              (For debugging) If non-null, process no more than this many tiles.
-	 * @param outputRecordComparator For sorting output records within a single tile.
-	 * @param codecPrototype         For spilling output records to disk.
-	 * @param outputRecordClass      Inconveniently needed to create SortingCollections.
-	 * @param includeNonPfReads      If true, will include ALL reads (including those which do not have PF set)
-     * @param ignoreUnexpectedBarcodes  If true, will ignore reads whose called barcode is not found in barcodeRecordWriterMap,
-     *                                  otherwise will throw an exception
-	 */
-	public IlluminaBasecallsConverter(final File basecallsDir, final int lane, final ReadStructure readStructure,
-	                                  final Map> barcodeRecordWriterMap,
-	                                  final boolean demultiplex,
-	                                  final int maxReadsInRamPerTile,
-	                                  final List tmpDirs,
-	                                  final int numProcessors, final boolean forceGc,
-	                                  final Integer firstTile, final Integer tileLimit,
-	                                  final Comparator outputRecordComparator,
-	                                  final SortingCollection.Codec codecPrototype,
-	                                  final Class outputRecordClass,
-	                                  final BclQualityEvaluationStrategy bclQualityEvaluationStrategy,
-	                                  final boolean applyEamssFiltering,
-	                                  final boolean includeNonPfReads,
+     * @param basecallsDir             Where to read basecalls from.
+     * @param lane                     What lane to process.
+     * @param readStructure            How to interpret each cluster.
+     * @param barcodeRecordWriterMap   Map from barcode to CLUSTER_OUTPUT_RECORD writer.  If demultiplex is false, must contain
+     *                                 one writer stored with key=null.
+     * @param demultiplex              If true, output is split by barcode, otherwise all are written to the same output stream.
+     * @param maxReadsInRamPerTile     Configures number of reads each tile will store in RAM before spilling to disk.
+     * @param tmpDirs                  For SortingCollection spilling.
+     * @param numProcessors            Controls number of threads.  If <= 0, the number of threads allocated is
+     *                                 available cores - numProcessors.
+     * @param forceGc                  Force explicit GC periodically.  This is good for causing memory maps to be released.
+     * @param firstTile                (For debugging) If non-null, start processing at this tile.
+     * @param tileLimit                (For debugging) If non-null, process no more than this many tiles.
+     * @param outputRecordComparator   For sorting output records within a single tile.
+     * @param codecPrototype           For spilling output records to disk.
+     * @param outputRecordClass        Inconveniently needed to create SortingCollections.
+     * @param includeNonPfReads        If true, will include ALL reads (including those which do not have PF set)
+     * @param ignoreUnexpectedBarcodes If true, will ignore reads whose called barcode is not found in barcodeRecordWriterMap,
+     *                                 otherwise will throw an exception
+     */
+    public IlluminaBasecallsConverter(final File basecallsDir, final int lane, final ReadStructure readStructure,
+                                      final Map> barcodeRecordWriterMap,
+                                      final boolean demultiplex,
+                                      final int maxReadsInRamPerTile,
+                                      final List tmpDirs,
+                                      final int numProcessors, final boolean forceGc,
+                                      final Integer firstTile, final Integer tileLimit,
+                                      final Comparator outputRecordComparator,
+                                      final SortingCollection.Codec codecPrototype,
+                                      final Class outputRecordClass,
+                                      final BclQualityEvaluationStrategy bclQualityEvaluationStrategy,
+                                      final boolean applyEamssFiltering,
+                                      final boolean includeNonPfReads,
                                       final boolean ignoreUnexpectedBarcodes
-	) {
-		this(basecallsDir, null, lane, readStructure,
-				barcodeRecordWriterMap, demultiplex, maxReadsInRamPerTile,
-				tmpDirs, numProcessors, forceGc, firstTile, tileLimit,
-				outputRecordComparator, codecPrototype, outputRecordClass,
-				bclQualityEvaluationStrategy, applyEamssFiltering,
-				includeNonPfReads, ignoreUnexpectedBarcodes);
-	}
-
-	/**
-     * @param basecallsDir           Where to read basecalls from.
-     * @param barcodesDir            Where to read barcodes from (optional; use basecallsDir if not specified).
-     * @param lane                   What lane to process.
-     * @param readStructure          How to interpret each cluster.
-     * @param barcodeRecordWriterMap Map from barcode to CLUSTER_OUTPUT_RECORD writer.  If demultiplex is false, must contain
-     *                               one writer stored with key=null.
-     * @param demultiplex            If true, output is split by barcode, otherwise all are written to the same output stream.
-     * @param maxReadsInRamPerTile   Configures number of reads each tile will store in RAM before spilling to disk.
-     * @param tmpDirs                For SortingCollection spilling.
-     * @param numProcessors          Controls number of threads.  If <= 0, the number of threads allocated is
-     *                               available cores - numProcessors.
-     * @param forceGc                Force explicit GC periodically.  This is good for causing memory maps to be released.
-     * @param firstTile              (For debugging) If non-null, start processing at this tile.
-     * @param tileLimit              (For debugging) If non-null, process no more than this many tiles.
-     * @param outputRecordComparator For sorting output records within a single tile.
-     * @param codecPrototype         For spilling output records to disk.
-     * @param outputRecordClass      Inconveniently needed to create SortingCollections.
-     * @param includeNonPfReads      If true, will include ALL reads (including those which do not have PF set)
-     * @param ignoreUnexpectedBarcodes  If true, will ignore reads whose called barcode is not found in barcodeRecordWriterMap,
-     *                                  otherwise will throw an exception
+    ) {
+        this(basecallsDir, null, lane, readStructure,
+                barcodeRecordWriterMap, demultiplex, maxReadsInRamPerTile,
+                tmpDirs, numProcessors, forceGc, firstTile, tileLimit,
+                outputRecordComparator, codecPrototype, outputRecordClass,
+                bclQualityEvaluationStrategy, applyEamssFiltering,
+                includeNonPfReads, ignoreUnexpectedBarcodes);
+    }
+
+    /**
+     * @param basecallsDir             Where to read basecalls from.
+     * @param barcodesDir              Where to read barcodes from (optional; use basecallsDir if not specified).
+     * @param lane                     What lane to process.
+     * @param readStructure            How to interpret each cluster.
+     * @param barcodeRecordWriterMap   Map from barcode to CLUSTER_OUTPUT_RECORD writer.  If demultiplex is false, must contain
+     *                                 one writer stored with key=null.
+     * @param demultiplex              If true, output is split by barcode, otherwise all are written to the same output stream.
+     * @param maxReadsInRamPerTile     Configures number of reads each tile will store in RAM before spilling to disk.
+     * @param tmpDirs                  For SortingCollection spilling.
+     * @param numProcessors            Controls number of threads.  If <= 0, the number of threads allocated is
+     *                                 available cores - numProcessors.
+     * @param forceGc                  Force explicit GC periodically.  This is good for causing memory maps to be released.
+     * @param firstTile                (For debugging) If non-null, start processing at this tile.
+     * @param tileLimit                (For debugging) If non-null, process no more than this many tiles.
+     * @param outputRecordComparator   For sorting output records within a single tile.
+     * @param codecPrototype           For spilling output records to disk.
+     * @param outputRecordClass        Inconveniently needed to create SortingCollections.
+     * @param includeNonPfReads        If true, will include ALL reads (including those which do not have PF set)
+     * @param ignoreUnexpectedBarcodes If true, will ignore reads whose called barcode is not found in barcodeRecordWriterMap,
+     *                                 otherwise will throw an exception
      */
     public IlluminaBasecallsConverter(final File basecallsDir, File barcodesDir, final int lane,
                                       final ReadStructure readStructure,
@@ -218,17 +177,18 @@ public IlluminaBasecallsConverter(final File basecallsDir, File barcodesDir, fin
                                       final boolean applyEamssFiltering, final boolean includeNonPfReads,
                                       final boolean ignoreUnexpectedBarcodes
     ) {
-        this.barcodeRecordWriterMap = barcodeRecordWriterMap;
-        this.demultiplex = demultiplex;
-        this.maxReadsInRamPerTile = maxReadsInRamPerTile;
-        this.tmpDirs = tmpDirs;
-        this.outputRecordComparator = outputRecordComparator;
-        this.codecPrototype = codecPrototype;
-        this.outputRecordClass = outputRecordClass;
-        this.bclQualityEvaluationStrategy = bclQualityEvaluationStrategy;
-        this.includeNonPfReads = includeNonPfReads;
-        this.ignoreUnexpectedBarcodes = ignoreUnexpectedBarcodes;
+        super(barcodeRecordWriterMap, maxReadsInRamPerTile, tmpDirs, codecPrototype, ignoreUnexpectedBarcodes,
+                demultiplex, outputRecordComparator, includeNonPfReads, bclQualityEvaluationStrategy, outputRecordClass,
+                numProcessors,
+                new IlluminaDataProviderFactory(basecallsDir, barcodesDir, lane, readStructure,
+                        bclQualityEvaluationStrategy, getDataTypesFromReadStructure(readStructure, demultiplex)));
+        this.tiles = factory.getAvailableTiles();
+        // Since the first non-fixed part of the read name is the tile number, without preceding zeroes,
+        // and the output is sorted by read name, process the tiles in this order.
+        tiles.sort(TILE_NUMBER_COMPARATOR);
+        setTileLimits(firstTile, tileLimit);
 
+        this.numThreads = Math.max(1, Math.min(this.numThreads, tiles.size()));
         // If we're forcing garbage collection, collect every 5 minutes in a daemon thread.
         if (forceGc) {
             final Timer gcTimer = new Timer(true);
@@ -247,67 +207,23 @@ public void run() {
             gcTimerTask = null;
         }
 
-        this.factory = new IlluminaDataProviderFactory(basecallsDir, barcodesDir, lane, readStructure, bclQualityEvaluationStrategy, getDataTypesFromReadStructure(readStructure, demultiplex));
         this.factory.setApplyEamssFiltering(applyEamssFiltering);
 
-        if (numProcessors == 0) {
-            this.numThreads = Runtime.getRuntime().availableProcessors();
-        } else if (numProcessors < 0) {
-            this.numThreads = Runtime.getRuntime().availableProcessors() + numProcessors;
-        } else {
-            this.numThreads = numProcessors;
-        }
-        this.tiles = new ArrayList(factory.getAvailableTiles());
-        // Since the first non-fixed part of the read name is the tile number, without preceding zeroes,
-        // and the output is sorted by read name, process the tiles in this order.
-        Collections.sort(tiles, TILE_NUMBER_COMPARATOR);
-        if (firstTile != null) {
-            int i;
-            for (i = 0; i < tiles.size(); ++i) {
-                if (tiles.get(i).intValue() == firstTile.intValue()) {
-                    tiles = tiles.subList(i, tiles.size());
-                    break;
-                }
-            }
-            if (tiles.get(0).intValue() != firstTile.intValue()) {
-                throw new PicardException("firstTile=" + firstTile + ", but that tile was not found.");
-            }
-        }
-        if (tileLimit != null && tiles.size() > tileLimit) {
-            tiles = tiles.subList(0, tileLimit);
-        }
-
-        this.numThreads = Math.max(1, Math.min(this.numThreads, tiles.size()));
-    }
-
-    /**
-     * Must be called before doTileProcessing.  This is not passed in the ctor because often the
-     * IlluminaDataProviderFactory is needed in order to construct the converter.
-     *
-     * @param converter Converts ClusterData to CLUSTER_OUTPUT_RECORD
-     */
-    public void setConverter(final ClusterDataConverter converter) {
-        this.converter = converter;
     }
 
-    /**
-     * In case caller needs to get some info from factory.
-     */
-    public IlluminaDataProviderFactory getFactory() {
-        return factory;
-    }
 
     /**
      * Do the work, i.e. create a bunch of threads to read, sort and write.
      * setConverter() must be called before calling this method.
      */
+    @Override
     public void doTileProcessing() {
         try {
             // TODO: Eliminate this when switch to JDK 7
             FileChannelJDKBugWorkAround.doBugWorkAround();
 
             // Generate the list of tiles that will be processed
-            final List tiles = new ArrayList();
+            final List tiles = new ArrayList<>();
             for (final Integer tileNumber : this.tiles) {
                 tiles.add(new Tile(tileNumber));
             }
@@ -330,7 +246,7 @@ public void doTileProcessing() {
 
         } finally {
             try {
-            	if (gcTimerTask != null) gcTimerTask.cancel();
+                if (gcTimerTask != null) gcTimerTask.cancel();
             } catch (final Throwable ex) {
                 log.warn(ex, "Ignoring exception stopping background GC thread.");
             }
@@ -389,7 +305,7 @@ public PriorityRunnable(final int priority) {
         /**
          * Returns the priority level.  Higher priorities are run earlier.
          *
-         * @return
+         * @return The priority for this runnable.
          */
         int getPriority() {
             return this.priority;
@@ -405,8 +321,8 @@ int getPriority() {
      */
     private class TileProcessingRecord {
         final private Map> barcodeToRecordCollection =
-                new HashMap>();
-        final private Map barcodeToProcessingState = new HashMap();
+                new HashMap<>();
+        final private Map barcodeToProcessingState = new HashMap<>();
         private TileProcessingState state = TileProcessingState.NOT_DONE_READING;
         private long recordCount = 0;
 
@@ -494,11 +410,7 @@ public synchronized TileBarcodeProcessingState getBarcodeState(final String barc
                         "A tile's barcode data's state cannot be queried until the tile has been completely read.");
             }
 
-            if (this.barcodeToProcessingState.containsKey(barcode)) {
-                return this.barcodeToProcessingState.get(barcode);
-            } else {
-                return TileBarcodeProcessingState.NA;
-            }
+            return this.barcodeToProcessingState.getOrDefault(barcode, TileBarcodeProcessingState.NA);
         }
 
         public synchronized Map getBarcodeProcessingStates() {
@@ -521,7 +433,7 @@ public synchronized void setBarcodeState(final String barcode, final TileBarcode
         /**
          * Returns the distinct set of barcodes for which data has been collected in this record.
          *
-         * @return
+         * @return The distinct set of barcodes for this record.
          */
         public synchronized Set getBarcodes() {
             return this.getBarcodeRecords().keySet();
@@ -548,7 +460,7 @@ public TileReader(final Tile tile, final TileReadAggregator handler, final TileP
          * this tile.
          */
         public void process() {
-            final IlluminaDataProvider dataProvider = factory.makeDataProvider(Arrays.asList(this.tile.getNumber()));
+            final BaseIlluminaDataProvider dataProvider = factory.makeDataProvider(Collections.singletonList(this.tile.getNumber()));
             log.debug(String.format("Reading data from tile %s ...", tile.getNumber()));
 
             while (dataProvider.hasNext()) {
@@ -577,29 +489,20 @@ public void process() {
          * 

          * Implemented as a TreeMap to guarantee tiles are iterated over in natural order.
          */
-        private final Map tileRecords = new TreeMap();
+        private final Map tileRecords = new TreeMap<>();
 
         /**
-         * The executor responsible for doing work.
-         * 

-         * Implemented as a ThreadPoolExecutor with a PriorityBlockingQueue which orders submitted Runnables by their
-         * priority.
+         * Compare the two Runnables, and assume they are PriorityRunnable; if not something strange is
+         * going on, so allow a ClassCastException be thrown.
          */
         private final ExecutorService prioritizingThreadPool = new ThreadPoolExecutor(
                 numThreads,
                 numThreads,
                 0L,
                 MILLISECONDS,
-                new PriorityBlockingQueue(5, new Comparator() {
-                    @Override
-                    /**
-                     * Compare the two Runnables, and assume they are PriorityRunnable; if not something strange is
-                     * going on, so allow a ClassCastException be thrown.
-                     */
-                    public int compare(final Runnable o1, final Runnable o2) {
-                        // Higher priority items go earlier in the queue, so reverse the "natural" comparison.
-                        return ((PriorityRunnable) o2).getPriority() - ((PriorityRunnable) o1).getPriority();
-                    }
+                new PriorityBlockingQueue<>(5, (o1, o2) -> {
+                    // Higher priority items go earlier in the queue, so reverse the "natural" comparison.
+                    return ((PriorityRunnable) o2).getPriority() - ((PriorityRunnable) o1).getPriority();
                 })
         );
 
@@ -619,7 +522,7 @@ public int compare(final Runnable o1, final Runnable o2) {
         /**
          * Creates a TileReadAggregator that reads from the provided tiles.
          *
-         * @param tiles
+         * @param tiles A collection of tiles to be read from.
          */
         public TileReadAggregator(final Collection tiles) {
             for (final Tile t : tiles) {
@@ -642,7 +545,7 @@ public void submit() {
             // Set the thread that is executing this work
             this.parentThread = Thread.currentThread();
 
-            /**
+            /*
              * For each tile, create and submit a tile processor.  Give it a negative execution priority (so that
              * prioritized tasks with a positive execution priority execute first), and give later tiles a lesser
              * (more negative) priority.
@@ -655,17 +558,14 @@ public void submit() {
                     public void run() {
                         try {
                             reader.process();
-                        } catch (final RuntimeException e) {
-                            /**
+                        } catch (final RuntimeException | Error e) {
+                            /*
                              * In the event of an internal failure, signal to the parent thread that something has gone
                              * wrong.  This is necessary because if an item of work fails to complete, the aggregator will
                              * will never reach its completed state, and it will never terminate.
                              */
                             parentThread.interrupt();
                             throw e;
-                        } catch (final Error e) {
-                            parentThread.interrupt();
-                            throw e;
                         }
                     }
                 });
@@ -702,7 +602,7 @@ private void completeTile(final Tile tile) {
         /**
          * Blocks until this aggregator completes its work.
          *
-         * @throws InterruptedException
+         * @throws InterruptedException is thrown when this executor has been interrupted.
          */
         public void awaitWorkComplete() throws InterruptedException {
             synchronized (this.completionLatch) {
@@ -726,21 +626,21 @@ private void signalWorkComplete() {
          */
         private void findAndEnqueueWorkOrSignalCompletion() {
             synchronized (this.workEnqueueMonitor) {
-                /**
+                /*
                  * If there is work remaining to be done in this aggregator, walk through all of the barcodes and find
                  * tiles which have not yet written their barcode data but are in a state where they are able to.
                  */
                 if (this.isWorkCompleted()) {
                     this.signalWorkComplete();
                 } else {
-                    final Queue tasks = new LinkedList();
+                    final Queue tasks = new LinkedList<>();
                     for (final String barcode : barcodeRecordWriterMap.keySet()) {
                         NEXT_BARCODE:
                         for (final Map.Entry entry : this.tileRecords.entrySet()) {
                             final Tile tile = entry.getKey();
                             final TileProcessingRecord tileRecord = entry.getValue();
 
-                            /**
+                            /*
                              * If this tile has not been read, we cannot write this or later tiles' barcode data;
                              * move to the next barcode.
                              */
@@ -750,20 +650,20 @@ private void findAndEnqueueWorkOrSignalCompletion() {
                             switch (tileRecord.getBarcodeState(barcode)) {
                                 case NA:
                                 case WRITTEN:
-                                    /**
+                                    /*
                                      * There is no data for this barcode for this tile, or it is already written; in
                                      * either scenario, this barcode will not be processed further for this tile, so
                                      * move onto the next tile as a possible candidate.
                                      */
                                     continue;
                                 case QUEUED_FOR_WRITE:
-                                    /**
+                                    /*
                                      * The write for this barcode is in progress for this tile, so skip to the next
                                      * barcode.
                                      */
                                     break NEXT_BARCODE;
                                 case READ:
-                                    /**
+                                    /*
                                      * This barcode has been read, and all of the earlier tiles have been written
                                      * for this barcode, so queue its writing.
                                      */
@@ -801,11 +701,11 @@ public void run() {
 
                         log.debug(String.format("Writing records from tile %s with barcode %s ...", tile.getNumber(), barcode));
 
-                        final PeekIterator it = new PeekIterator(records.iterator());
+                        final PeekIterator it = new PeekIterator<>(records.iterator());
                         while (it.hasNext()) {
                             final CLUSTER_OUTPUT_RECORD rec = it.next();
 
-                            /**
+                            /*
                              * PIC-330 Sometimes there are two reads with the same cluster coordinates, and thus
                              * the same read name.  Discard both of them.  This code assumes that the two first of pairs
                              * will come before the two second of pairs, so it isn't necessary to look ahead a different
@@ -835,17 +735,14 @@ public void run() {
                         tileRecord.setBarcodeState(barcode, TileBarcodeProcessingState.WRITTEN);
                         findAndEnqueueWorkOrSignalCompletion();
 
-                    } catch (final RuntimeException e) {
-                        /**
+                    } catch (final RuntimeException | Error e) {
+                        /*
                          * In the event of an internal failure, signal to the parent thread that something has gone
                          * wrong.  This is necessary because if an item of work fails to complete, the aggregator will
                          * will never reach its completed state, and it will never terminate.
                          */
                         parentThread.interrupt();
                         throw e;
-                    } catch (final Error e) {
-                        parentThread.interrupt();
-                        throw e;
                     }
                 }
 
@@ -899,17 +796,4 @@ public void shutdown() {
         }
     }
 
-    public static interface ClusterDataConverter {
-
-        /**
-         * Creates the OUTPUT_RECORDs from the cluster
-         */
-        public OUTPUT_RECORD convertClusterToOutputRecord(final ClusterData cluster);
-    }
-
-    public static interface ConvertedClusterDataWriter {
-        void write(final OUTPUT_RECORD rec);
-
-        void close();
-    }
 }
diff --git a/src/main/java/picard/illumina/IlluminaBasecallsToFastq.java b/src/main/java/picard/illumina/IlluminaBasecallsToFastq.java
index 43ade8161..da3df57df 100644
--- a/src/main/java/picard/illumina/IlluminaBasecallsToFastq.java
+++ b/src/main/java/picard/illumina/IlluminaBasecallsToFastq.java
@@ -30,6 +30,7 @@
 import htsjdk.samtools.fastq.FastqRecord;
 import htsjdk.samtools.fastq.FastqWriter;
 import htsjdk.samtools.fastq.FastqWriterFactory;
+import htsjdk.samtools.metrics.MetricsFile;
 import htsjdk.samtools.util.CollectionUtil;
 import htsjdk.samtools.util.IOUtil;
 import htsjdk.samtools.util.Log;
@@ -39,11 +40,12 @@
 import picard.cmdline.CommandLineProgram;
 import picard.cmdline.CommandLineProgramProperties;
 import picard.cmdline.Option;
-import picard.cmdline.programgroups.Illumina;
 import picard.cmdline.StandardOptionDefinitions;
+import picard.cmdline.programgroups.Illumina;
 import picard.fastq.Casava18ReadNameEncoder;
 import picard.fastq.IlluminaReadNameEncoder;
 import picard.fastq.ReadNameEncoder;
+import picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric;
 import picard.illumina.parser.ClusterData;
 import picard.illumina.parser.ReadData;
 import picard.illumina.parser.ReadStructure;
@@ -58,7 +60,6 @@
 import java.io.OutputStream;
 import java.io.PrintStream;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.Comparator;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -68,57 +69,57 @@
 import java.util.Set;
 
 @CommandLineProgramProperties(
-  usage = IlluminaBasecallsToFastq.USAGE_SUMMARY + IlluminaBasecallsToFastq.USAGE_DETAILS,
-  usageShort = IlluminaBasecallsToFastq.USAGE_SUMMARY,
-  programGroup = Illumina.class
+        usage = IlluminaBasecallsToFastq.USAGE_SUMMARY + IlluminaBasecallsToFastq.USAGE_DETAILS,
+        usageShort = IlluminaBasecallsToFastq.USAGE_SUMMARY,
+        programGroup = Illumina.class
 )
 public class IlluminaBasecallsToFastq extends CommandLineProgram {
-  static final String USAGE_SUMMARY = "Generate FASTQ file(s) from Illumina basecall read data.  ";
-  static final String USAGE_DETAILS = "
This tool generates FASTQ files from data in an Illumina BaseCalls output directory.  " +
-          "Separate FASTQ files are created for each template, barcode, and index (molecular barcode) read.  Briefly, the template reads " +
-          "are the target sequence of your experiment, the barcode sequence reads facilitate sample demultiplexing, and the index reads " +
-          "help mitigate instrument phasing errors.  For additional information on the read types, please see the following " +
-          "reference here.
" +
-          "" +
-          "
In the absence of sample pooling (multiplexing) and/or barcodes, then an OUTPUT_PREFIX (file directory) must be " +
-          "provided as the sample identifier.  For multiplexed samples, a MULTIPLEX_PARAMS file must be specified.  " +
-          "The MULTIPLEX_PARAMS file contains the list of sample barcodes used to sort template, barcode, and index reads.  " +
-          "It is essentially the same as the BARCODE_FILE used in the" +
-          "ExtractIlluminaBarcodes " +
-          "tool.
     "+
-          "" +
-          "
Files from this tool use the following naming format: {prefix}.{type}_{number}.fastq with the {prefix} indicating the sample " +
-          "barcode, the {type} indicating the types of reads e.g. index, barcode, or blank (if it contains a template read).  " +
-          "The {number} indicates the read number, either first (1) or second (2) for paired-end sequencing. 
 " +
-
-"
Usage examples:
" +
-"
" +
-"Example 1: Sample(s) with either no barcode or barcoded without multiplexing 
" +
-"java -jar picard.jar IlluminaBasecallsToFastq \\
"+
-"      READ_STRUCTURE=25T8B25T \\
"+
-"      BASECALLS_DIR=basecallDirectory \\
"+
-"      LANE=001 \\
"+
-"      OUTPUT_PREFIX=noBarcode.1 \\
"+
-"      RUN_BARCODE=run15 \\
"+
-"      FLOWCELL_BARCODE=abcdeACXX 

" +
-
-"Example 2: Multiplexed samples 
" +
-"java -jar picard.jar IlluminaBasecallsToFastq \\
"+
-"      READ_STRUCTURE=25T8B25T \\
"+
-"      BASECALLS_DIR=basecallDirectory \\
"+
-"      LANE=001 \\
"+
-"      MULTIPLEX_PARAMS=demultiplexed_output.txt \\
"+
-"      RUN_BARCODE=run15 \\
"+
-"      FLOWCELL_BARCODE=abcdeACXX 
" +
-"
"+
-"
The FLOWCELL_BARCODE is required if emitting Casava 1.8-style read name headers.
" +
-          "
"
-;
+    static final String USAGE_SUMMARY = "Generate FASTQ file(s) from Illumina basecall read data.  ";
+    static final String USAGE_DETAILS = "
This tool generates FASTQ files from data in an Illumina BaseCalls output directory.  " +
+            "Separate FASTQ files are created for each template, barcode, and index (molecular barcode) read.  Briefly, the template reads " +
+            "are the target sequence of your experiment, the barcode sequence reads facilitate sample demultiplexing, and the index reads " +
+            "help mitigate instrument phasing errors.  For additional information on the read types, please see the following " +
+            "reference here.
" +
+            "" +
+            "
In the absence of sample pooling (multiplexing) and/or barcodes, then an OUTPUT_PREFIX (file directory) must be " +
+            "provided as the sample identifier.  For multiplexed samples, a MULTIPLEX_PARAMS file must be specified.  " +
+            "The MULTIPLEX_PARAMS file contains the list of sample barcodes used to sort template, barcode, and index reads.  " +
+            "It is essentially the same as the BARCODE_FILE used in the" +
+            "ExtractIlluminaBarcodes " +
+            "tool.
     " +
+            "" +
+            "
Files from this tool use the following naming format: {prefix}.{type}_{number}.fastq with the {prefix} indicating the sample " +
+            "barcode, the {type} indicating the types of reads e.g. index, barcode, or blank (if it contains a template read).  " +
+            "The {number} indicates the read number, either first (1) or second (2) for paired-end sequencing. 
 " +
+
+            "
Usage examples:
" +
+            "
" +
+            "Example 1: Sample(s) with either no barcode or barcoded without multiplexing 
" +
+            "java -jar picard.jar IlluminaBasecallsToFastq \\
" +
+            "      READ_STRUCTURE=25T8B25T \\
" +
+            "      BASECALLS_DIR=basecallDirectory \\
" +
+            "      LANE=001 \\
" +
+            "      OUTPUT_PREFIX=noBarcode.1 \\
" +
+            "      RUN_BARCODE=run15 \\
" +
+            "      FLOWCELL_BARCODE=abcdeACXX 

" +
+
+            "Example 2: Multiplexed samples 
" +
+            "java -jar picard.jar IlluminaBasecallsToFastq \\
" +
+            "      READ_STRUCTURE=25T8B25T \\
" +
+            "      BASECALLS_DIR=basecallDirectory \\
" +
+            "      LANE=001 \\
" +
+            "      MULTIPLEX_PARAMS=demultiplexed_output.txt \\
" +
+            "      RUN_BARCODE=run15 \\
" +
+            "      FLOWCELL_BARCODE=abcdeACXX 
" +
+            "
" +
+            "
The FLOWCELL_BARCODE is required if emitting Casava 1.8-style read name headers.
" +
+            "
";
+
     // The following attributes define the command-line arguments
 
     @Option(doc = "The basecalls directory. ", shortName = "B")
     public File BASECALLS_DIR;
-    
+
     @Option(doc = "The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If not set, use BASECALLS_DIR. ", shortName = "BCD", optional = true)
     public File BARCODES_DIR;
 
@@ -131,15 +132,15 @@
             mutex = {"MULTIPLEX_PARAMS"})
     public File OUTPUT_PREFIX;
 
-    @Option(doc = "The barcode of the run.  Prefixed to read names.", optional = false)
+    @Option(doc = "The barcode of the run.  Prefixed to read names.")
     public String RUN_BARCODE;
 
     @Option(doc = "The name of the machine on which the run was sequenced; required if emitting Casava1.8-style read name headers", optional = true)
     public String MACHINE_NAME;
-    
+
     @Option(doc = "The barcode of the flowcell that was sequenced; required if emitting Casava1.8-style read name headers", optional = true)
     public String FLOWCELL_BARCODE;
-    
+
     @Option(doc = ReadStructure.PARAMETER_DOC, shortName = "RS")
     public String READ_STRUCTURE;
 
@@ -167,7 +168,7 @@
     @Option(doc = "If set, process no more than this many tiles (used for debugging).", optional = true)
     public Integer TILE_LIMIT;
 
-    @Option(doc="Apply EAMSS filtering to identify inappropriately quality scored bases towards the ends of reads" +
+    @Option(doc = "Apply EAMSS filtering to identify inappropriately quality scored bases towards the ends of reads" +
             " and convert their quality scores to Q2.")
     public boolean APPLY_EAMSS_FILTER = true;
 
@@ -179,32 +180,49 @@
             " run, each SortingCollection gets this value/number of indices.")
     public int MAX_READS_IN_RAM_PER_TILE = 1200000;
 
-    @Option(doc="The minimum quality (after transforming 0s to 1s) expected from reads.  If qualities are lower than this value, an error is thrown." +
+    @Option(doc = "The minimum quality (after transforming 0s to 1s) expected from reads.  If qualities are lower than this value, an error is thrown." +
             "The default of 2 is what the Illumina's spec describes as the minimum, but in practice the value has been observed lower.")
     public int MINIMUM_QUALITY = BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY;
 
-    @Option(doc="Whether to include non-PF reads", shortName="NONPF", optional=true)
+    @Option(doc = "Whether to include non-PF reads", shortName = "NONPF", optional = true)
     public boolean INCLUDE_NON_PF_READS = true;
 
-    @Option(doc="Whether to ignore reads whose barcodes are not found in MULTIPLEX_PARAMS.  Useful when outputting " +
-            "FASTQs for only a subset of the barcodes in a lane.", shortName="INGORE_UNEXPECTED")
+    @Option(doc = "Whether to ignore reads whose barcodes are not found in MULTIPLEX_PARAMS.  Useful when outputting " +
+            "FASTQs for only a subset of the barcodes in a lane.", shortName = "INGORE_UNEXPECTED")
     public boolean IGNORE_UNEXPECTED_BARCODES = false;
 
-    @Option(doc="The read name header formatting to emit.  Casava1.8 formatting has additional information beyond Illumina, including: " +
-            "the passing-filter flag value for the read, the flowcell name, and the sequencer name.", optional = false)
+    @Option(doc = "The read name header formatting to emit.  Casava1.8 formatting has additional information beyond Illumina, including: " +
+            "the passing-filter flag value for the read, the flowcell name, and the sequencer name.")
     public ReadNameFormat READ_NAME_FORMAT = ReadNameFormat.CASAVA_1_8;
 
     @Option(shortName = "GZIP", doc = "Compress output FASTQ files using gzip and append a .gz extension to the file names.")
     public boolean COMPRESS_OUTPUTS = false;
 
-    /** Simple switch to control the read name format to emit. */
+    @Option(doc = "Use the new converter", optional = true)
+    public boolean USE_NEW_CONVERTER = false;
+
+    @Option(doc = "Maximum mismatches for a barcode to be considered a match.")
+    public int MAX_MISMATCHES = 1;
+
+    @Option(doc = "Minimum difference between number of mismatches in the best and second best barcodes for a barcode to be considered a match.")
+    public int MIN_MISMATCH_DELTA = 1;
+
+    @Option(doc = "Maximum allowable number of no-calls in a barcode read before it is considered unmatchable.")
+    public int MAX_NO_CALLS = 2;
+
+    @Option(doc = "Per-barcode and per-lane metrics written to this file.", shortName = StandardOptionDefinitions.METRICS_FILE_SHORT_NAME, optional = true)
+    public File METRICS_FILE;
+
+    /**
+     * Simple switch to control the read name format to emit.
+     */
     public enum ReadNameFormat {
         CASAVA_1_8, ILLUMINA
     }
-    
+
     private final Map sampleBarcodeFastqWriterMap = new HashMap<>();
     private ReadStructure readStructure;
-    IlluminaBasecallsConverter basecallsConverter;
+    private BasecallsConverter basecallsConverter;
     private static final Log log = Log.getInstance(IlluminaBasecallsToFastq.class);
     private final FastqWriterFactory fastqWriterFactory = new FastqWriterFactory();
     private ReadNameEncoder readNameEncoder;
@@ -214,15 +232,13 @@
     @Override
     protected int doWork() {
         initialize();
-
         basecallsConverter.doTileProcessing();
-
         return 0;
     }
 
     @Override
     protected String[] customCommandLineValidation() {
-        final LinkedList errors = new LinkedList();
+        final LinkedList errors = new LinkedList<>();
         if (READ_NAME_FORMAT == ReadNameFormat.CASAVA_1_8 && MACHINE_NAME == null) {
             errors.add("MACHINE_NAME is required when using Casava1.8-style read name headers.");
         }
@@ -234,7 +250,7 @@ protected int doWork() {
         if (ADAPTERS_TO_CHECK != null) {
             log.warn("ADAPTERS_TO_CHECK is not used");
         }
-        
+
         if (errors.isEmpty()) {
             return null;
         } else {
@@ -249,13 +265,13 @@ private void initialize() {
         fastqWriterFactory.setCreateMd5(CREATE_MD5_FILE);
         switch (READ_NAME_FORMAT) {
             case CASAVA_1_8:
-                readNameEncoder = new Casava18ReadNameEncoder(MACHINE_NAME, RUN_BARCODE, FLOWCELL_BARCODE);        
+                readNameEncoder = new Casava18ReadNameEncoder(MACHINE_NAME, RUN_BARCODE, FLOWCELL_BARCODE);
                 break;
             case ILLUMINA:
                 readNameEncoder = new IlluminaReadNameEncoder(RUN_BARCODE);
                 break;
         }
-        
+
         final BclQualityEvaluationStrategy bclQualityEvaluationStrategy = new BclQualityEvaluationStrategy(MINIMUM_QUALITY);
         readStructure = new ReadStructure(READ_STRUCTURE);
         if (MULTIPLEX_PARAMS != null) {
@@ -270,18 +286,38 @@ private void initialize() {
             demultiplex = true;
         }
         final int readsPerCluster = readStructure.templates.length() + readStructure.sampleBarcodes.length();
-        basecallsConverter = new IlluminaBasecallsConverter<>(BASECALLS_DIR, BARCODES_DIR, LANE, readStructure,
-                sampleBarcodeFastqWriterMap, demultiplex, Math.max(1, MAX_READS_IN_RAM_PER_TILE / readsPerCluster), TMP_DIR, NUM_PROCESSORS,
-                FORCE_GC, FIRST_TILE, TILE_LIMIT, queryNameComparator,
-                new FastqRecordsForClusterCodec(readStructure.templates.length(),
-                        readStructure.sampleBarcodes.length(), readStructure.molecularBarcode.length()), FastqRecordsForCluster.class, bclQualityEvaluationStrategy,
-                this.APPLY_EAMSS_FILTER, INCLUDE_NON_PF_READS, IGNORE_UNEXPECTED_BARCODES);
+        if (USE_NEW_CONVERTER) {
+            if (METRICS_FILE != null) {
+                IOUtil.assertFileIsWritable(METRICS_FILE);
+            } else {
+                log.warn("No METRICS_FILE specified. Barcode metrics will not be generated.");
+            }
 
-        log.info("READ STRUCTURE IS " + readStructure.toString());
+            final MetricsFile metricsFile = getMetricsFile();
+
+            basecallsConverter = new NewIlluminaBasecallsConverter<>(BASECALLS_DIR, BARCODES_DIR, LANE, readStructure,
+                    sampleBarcodeFastqWriterMap, demultiplex, Math.max(1, MAX_READS_IN_RAM_PER_TILE / readsPerCluster),
+                    TMP_DIR, NUM_PROCESSORS,
+                    FIRST_TILE, TILE_LIMIT, queryNameComparator,
+                    new FastqRecordsForClusterCodec(readStructure.templates.length(),
+                            readStructure.sampleBarcodes.length(), readStructure.molecularBarcode.length()),
+                    FastqRecordsForCluster.class, bclQualityEvaluationStrategy,
+                    this.APPLY_EAMSS_FILTER, INCLUDE_NON_PF_READS, IGNORE_UNEXPECTED_BARCODES, MAX_NO_CALLS,
+                    MAX_MISMATCHES, MIN_MISMATCH_DELTA, MINIMUM_QUALITY, metricsFile, METRICS_FILE);
+        } else {
+            basecallsConverter = new IlluminaBasecallsConverter<>(BASECALLS_DIR, BARCODES_DIR, LANE, readStructure,
+                    sampleBarcodeFastqWriterMap, demultiplex, Math.max(1, MAX_READS_IN_RAM_PER_TILE / readsPerCluster), TMP_DIR, NUM_PROCESSORS,
+                    FORCE_GC, FIRST_TILE, TILE_LIMIT, queryNameComparator,
+                    new FastqRecordsForClusterCodec(readStructure.templates.length(),
+                            readStructure.sampleBarcodes.length(), readStructure.molecularBarcode.length()), FastqRecordsForCluster.class, bclQualityEvaluationStrategy,
+                    this.APPLY_EAMSS_FILTER, INCLUDE_NON_PF_READS, IGNORE_UNEXPECTED_BARCODES);
+        }
 
         basecallsConverter.setConverter(
                 new ClusterToFastqRecordsForClusterConverter(
                         basecallsConverter.getFactory().getOutputReadStructure()));
+
+        log.info("READ STRUCTURE IS " + readStructure.toString());
     }
 
     /**
@@ -298,7 +334,7 @@ private void assertExpectedColumns(final Set actualCols, final Set {
+    private static final class FastqRecordsWriter implements BasecallsConverter.ConvertedClusterDataWriter {
         final FastqWriter[] templateWriters;
         final FastqWriter[] sampleBarcodeWriters;
         final FastqWriter[] molecularBarcodeWriters;
 
         /**
-         * @param templateWriters Writers for template reads in order, e,g. 0th element is for template read 1.
-         * @param sampleBarcodeWriters Writers for sample barcode reads in order, e,g. 0th element is for sample barcode read 1.
+         * @param templateWriters         Writers for template reads in order, e,g. 0th element is for template read 1.
+         * @param sampleBarcodeWriters    Writers for sample barcode reads in order, e,g. 0th element is for sample barcode read 1.
          * @param molecularBarcodeWriters Writers for molecular barcode reads in order, e,g. 0th element is for molecualr barcode read 1.
          */
         private FastqRecordsWriter(final FastqWriter[] templateWriters, final FastqWriter[] sampleBarcodeWriters, final FastqWriter[] molecularBarcodeWriters) {
-            this.templateWriters         = templateWriters;
-            this.sampleBarcodeWriters    = sampleBarcodeWriters;
+            this.templateWriters = templateWriters;
+            this.sampleBarcodeWriters = sampleBarcodeWriters;
             this.molecularBarcodeWriters = molecularBarcodeWriters;
         }
 
         @Override
         public void write(final FastqRecordsForCluster records) {
-            write(templateWriters,         records.templateRecords);
-            write(sampleBarcodeWriters,    records.sampleBarcodeRecords);
+            write(templateWriters, records.templateRecords);
+            write(sampleBarcodeWriters, records.sampleBarcodeRecords);
             write(molecularBarcodeWriters, records.molecularBarcodeRecords);
         }
 
@@ -434,8 +470,8 @@ public void close() {
         final FastqRecord[] molecularBarcodeRecords;
 
         FastqRecordsForCluster(final int numTemplates, final int numSampleBarcodes, final int numMolecularBarcodes) {
-            templateRecords         = new FastqRecord[numTemplates];
-            sampleBarcodeRecords    = new FastqRecord[numSampleBarcodes];
+            templateRecords = new FastqRecord[numTemplates];
+            sampleBarcodeRecords = new FastqRecord[numSampleBarcodes];
             molecularBarcodeRecords = new FastqRecord[numMolecularBarcodes];
         }
     }
@@ -446,13 +482,13 @@ public void close() {
     class ClusterToFastqRecordsForClusterConverter
             implements IlluminaBasecallsConverter.ClusterDataConverter {
 
-        private final int [] templateIndices;
-        private final int [] sampleBarcodeIndicies;
-        private final int [] molecularBarcodeIndicies;
+        private final int[] templateIndices;
+        private final int[] sampleBarcodeIndicies;
+        private final int[] molecularBarcodeIndicies;
 
         ClusterToFastqRecordsForClusterConverter(final ReadStructure outputReadStructure) {
-            this.templateIndices          = outputReadStructure.templates.getIndices();
-            this.sampleBarcodeIndicies    = outputReadStructure.sampleBarcodes.getIndices();
+            this.templateIndices = outputReadStructure.templates.getIndices();
+            this.sampleBarcodeIndicies = outputReadStructure.sampleBarcodes.getIndices();
             this.molecularBarcodeIndicies = outputReadStructure.molecularBarcode.getIndices();
         }
 
@@ -462,8 +498,8 @@ public FastqRecordsForCluster convertClusterToOutputRecord(final ClusterData clu
             final boolean appendTemplateNumberSuffix = ret.templateRecords.length > 1;
             final boolean appendMolecularBarcodeNumber = ret.molecularBarcodeRecords.length > 1;
 
-            makeFastqRecords(ret.templateRecords,         templateIndices,          cluster, appendTemplateNumberSuffix);
-            makeFastqRecords(ret.sampleBarcodeRecords,    sampleBarcodeIndicies,    cluster, false);
+            makeFastqRecords(ret.templateRecords, templateIndices, cluster, appendTemplateNumberSuffix);
+            makeFastqRecords(ret.sampleBarcodeRecords, sampleBarcodeIndicies, cluster, false);
             makeFastqRecords(ret.molecularBarcodeRecords, molecularBarcodeIndicies, cluster, appendMolecularBarcodeNumber);
 
             return ret;
@@ -476,8 +512,8 @@ private void makeFastqRecords(final FastqRecord[] recs, final int[] indices,
                 final String readBases = StringUtil.bytesToString(readData.getBases()).replace('.', 'N');
                 final String readName = readNameEncoder.generateReadName(cluster, appendReadNumberSuffix ? i + 1 : null);
                 recs[i] = new FastqRecord(
-                        readName, 
-                        readBases, 
+                        readName,
+                        readBases,
                         null,
                         SAMUtils.phredToFastq(readData.getQualities())
                 );
@@ -524,7 +560,7 @@ public void encode(final FastqRecordsForCluster val) {
         }
 
         private void encodeArray(final FastqRecord[] recs) {
-            for (final FastqRecord rec: recs) {
+            for (final FastqRecord rec : recs) {
                 writer.write(rec);
             }
         }
diff --git a/src/main/java/picard/illumina/IlluminaBasecallsToSam.java b/src/main/java/picard/illumina/IlluminaBasecallsToSam.java
index f31c5ecac..577969bcd 100644
--- a/src/main/java/picard/illumina/IlluminaBasecallsToSam.java
+++ b/src/main/java/picard/illumina/IlluminaBasecallsToSam.java
@@ -31,6 +31,7 @@
 import htsjdk.samtools.SAMReadGroupRecord;
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.SAMRecordQueryNameComparator;
+import htsjdk.samtools.metrics.MetricsFile;
 import htsjdk.samtools.util.CollectionUtil;
 import htsjdk.samtools.util.IOUtil;
 import htsjdk.samtools.util.Iso8601Date;
@@ -41,8 +42,9 @@
 import picard.cmdline.CommandLineProgram;
 import picard.cmdline.CommandLineProgramProperties;
 import picard.cmdline.Option;
-import picard.cmdline.programgroups.Illumina;
 import picard.cmdline.StandardOptionDefinitions;
+import picard.cmdline.programgroups.Illumina;
+import picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric;
 import picard.illumina.parser.ReadStructure;
 import picard.illumina.parser.readers.BclQualityEvaluationStrategy;
 import picard.util.AdapterPair;
@@ -80,7 +82,7 @@
  * reading Illumina data for their respective tiles from disk, and as they collect that data, it is fed back into the
  * TileReadAggregator.  When a TileReader completes a tile, it notifies the TileReadAggregator, which reviews what was
  * read and conditionally queues its writing to disk, baring in mind the requirements of write-order described in the
- * previous paragraph.  As writes complete, the TileReadAggregator re-evalutes the state of reads/writes and may queue
+ * previous paragraph.  As writes complete, the TileReadAggregator re-evaluates the state of reads/writes and may queue
  * more writes.  When all barcodes for all tiles have been written, the TileReadAggregator shuts down.
  * 

  * The TileReadAggregator controls task execution using a specialized ThreadPoolExecutor.  It accepts special Runnables
@@ -99,12 +101,12 @@
         programGroup = Illumina.class
 )
 public class IlluminaBasecallsToSam extends CommandLineProgram {
-    static final String USAGE_SUMMARY = "Transforms raw Illumina sequencing data into an unmapped SAM or BAM file."  ;
+    static final String USAGE_SUMMARY = "Transforms raw Illumina sequencing data into an unmapped SAM or BAM file.";
     static final String USAGE_DETAILS = "
The IlluminaBaseCallsToSam program collects, demultiplexes, and sorts reads across all " +
             "of the tiles of a lane via barcode to produce an unmapped SAM/BAM file.  An unmapped BAM file is often referred to as a uBAM.  " +
             "All barcode, sample, and library data is provided in the LIBRARY_PARAMS file.  Note, this LIBRARY_PARAMS file " +
             "should be formatted according to the specifications indicated below.  The following is an example of a properly" +
-            " formmated LIBRARY_PARAMS file:
" +
+            " formatted LIBRARY_PARAMS file:
" +
             "BARCODE_1\tOUTPUT\tSAMPLE_ALIAS\tLIBRARY_NAME\n" +
             "AAAAAAAA\tSA_AAAAAAAA.bam\tSA_AAAAAAAA\tLN_AAAAAAAA\n" +
             "AAAAGAAG\tSA_AAAAGAAG.bam\tSA_AAAAGAAG\tLN_AAAAGAAG\n" +
@@ -126,8 +128,7 @@
             "      IGNORE_UNEXPECTED_BARCODES=true \\
" +
             "      LIBRARY_PARAMS=library.params " +
             "
" + - "
" - ; + "
"; // The following attributes define the command-line arguments @@ -136,7 +137,7 @@ @Option(doc = "The basecalls directory. ", shortName = "B") public File BASECALLS_DIR; - + @Option(doc = "The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If not set, use BASECALLS_DIR. ", shortName = "BCD", optional = true) public File BARCODES_DIR; @@ -196,7 +197,7 @@ public File LIBRARY_PARAMS; @Option(doc = "Which adapters to look for in the read.") - public List ADAPTERS_TO_CHECK = new ArrayList( + public List ADAPTERS_TO_CHECK = new ArrayList<>( Arrays.asList(IlluminaAdapterPair.INDEXED, IlluminaAdapterPair.DUAL_INDEXED, IlluminaAdapterPair.NEXTERA_V2, @@ -225,7 +226,7 @@ "is larger than the available memory.") public Boolean FORCE_GC = true; - @Option(doc="Apply EAMSS filtering to identify inappropriately quality scored bases towards the ends of reads" + + @Option(doc = "Apply EAMSS filtering to identify inappropriately quality scored bases towards the ends of reads" + " and convert their quality scores to Q2.") public boolean APPLY_EAMSS_FILTER = true; @@ -233,32 +234,47 @@ " run, each SortingCollection gets this value/number of indices.") public int MAX_READS_IN_RAM_PER_TILE = 1200000; - @Option(doc="The minimum quality (after transforming 0s to 1s) expected from reads. If qualities are lower than this value, an error is thrown." + + @Option(doc = "The minimum quality (after transforming 0s to 1s) expected from reads. If qualities are lower than this value, an error is thrown." + "The default of 2 is what the Illumina's spec describes as the minimum, but in practice the value has been observed lower.") public int MINIMUM_QUALITY = BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY; - @Option(doc="Whether to include non-PF reads", shortName="NONPF", optional=true) + @Option(doc = "Whether to include non-PF reads", shortName = "NONPF", optional = true) public boolean INCLUDE_NON_PF_READS = true; - @Option(doc="Whether to ignore reads whose barcodes are not found in LIBRARY_PARAMS. Useful when outputting " + - "BAMs for only a subset of the barcodes in a lane.", shortName="IGNORE_UNEXPECTED") + @Option(doc = "Whether to ignore reads whose barcodes are not found in LIBRARY_PARAMS. Useful when outputting " + + "BAMs for only a subset of the barcodes in a lane.", shortName = "IGNORE_UNEXPECTED") public boolean IGNORE_UNEXPECTED_BARCODES = false; - @Option(doc="The tag to use to store any molecular indexes. If more than one molecular index is found, they will be concatenated and stored here.", optional=true) + @Option(doc = "The tag to use to store any molecular indexes. If more than one molecular index is found, they will be concatenated and stored here.", optional = true) public String MOLECULAR_INDEX_TAG = "RX"; - @Option(doc="The tag to use to store any molecular index base qualities. If more than one molecular index is found, their qualities will be concatenated and stored here " + - "(.i.e. the number of \"M\" operators in the READ_STRUCTURE)", optional=true) + @Option(doc = "The tag to use to store any molecular index base qualities. If more than one molecular index is found, their qualities will be concatenated and stored here " + + "(.i.e. the number of \"M\" operators in the READ_STRUCTURE)", optional = true) public String MOLECULAR_INDEX_BASE_QUALITY_TAG = "QX"; - @Option(doc="The list of tags to store each molecular index. The number of tags should match the number of molecular indexes.", optional=true) + @Option(doc = "The list of tags to store each molecular index. The number of tags should match the number of molecular indexes.", optional = true) public List TAG_PER_MOLECULAR_INDEX; - private final Map barcodeSamWriterMap = new HashMap(); + @Option(doc = "Use the new converter", optional = true) + public boolean USE_NEW_CONVERTER = false; + + @Option(doc = "Maximum mismatches for a barcode to be considered a match.") + public int MAX_MISMATCHES = 1; + + @Option(doc = "Minimum difference between number of mismatches in the best and second best barcodes for a barcode to be considered a match.") + public int MIN_MISMATCH_DELTA = 1; + + @Option(doc = "Maximum allowable number of no-calls in a barcode read before it is considered unmatchable.") + public int MAX_NO_CALLS = 2; + + + @Option(doc = "Per-barcode and per-lane metrics written to this file.", shortName = StandardOptionDefinitions.METRICS_FILE_SHORT_NAME, optional = true) + public File METRICS_FILE; + + private final Map barcodeSamWriterMap = new HashMap<>(); private ReadStructure readStructure; - IlluminaBasecallsConverter basecallsConverter; + private BasecallsConverter basecallsConverter; private static final Log log = Log.getInstance(IlluminaBasecallsToSam.class); - private BclQualityEvaluationStrategy bclQualityEvaluationStrategy; @Override protected int doWork() { @@ -271,7 +287,7 @@ protected int doWork() { * Prepares loggers, initiates garbage collection thread, parses arguments and initialized variables appropriately/ */ private void initialize() { - this.bclQualityEvaluationStrategy = new BclQualityEvaluationStrategy(MINIMUM_QUALITY); + BclQualityEvaluationStrategy bclQualityEvaluationStrategy = new BclQualityEvaluationStrategy(MINIMUM_QUALITY); if (OUTPUT != null) { IOUtil.assertFileIsWritable(OUTPUT); @@ -282,20 +298,12 @@ private void initialize() { } if (OUTPUT != null) { - barcodeSamWriterMap.put(null, buildSamFileWriter(OUTPUT, SAMPLE_ALIAS, LIBRARY_NAME, buildSamHeaderParameters(null))); + barcodeSamWriterMap.put(null, buildSamFileWriter(OUTPUT, SAMPLE_ALIAS, LIBRARY_NAME, buildSamHeaderParameters(null), !USE_NEW_CONVERTER)); } else { populateWritersFromLibraryParams(); } final int numOutputRecords = readStructure.templates.length(); - - basecallsConverter = new IlluminaBasecallsConverter(BASECALLS_DIR, BARCODES_DIR, LANE, readStructure, - barcodeSamWriterMap, true, MAX_READS_IN_RAM_PER_TILE/numOutputRecords, TMP_DIR, NUM_PROCESSORS, FORCE_GC, - FIRST_TILE, TILE_LIMIT, new QueryNameComparator(), new Codec(numOutputRecords), SAMRecordsForCluster.class, - bclQualityEvaluationStrategy, this.APPLY_EAMSS_FILTER, INCLUDE_NON_PF_READS, IGNORE_UNEXPECTED_BARCODES); - - log.info("DONE_READING STRUCTURE IS " + readStructure.toString()); - // Combine any adapters and custom adapter pairs from the command line into an array for use in clipping final List adapters = new ArrayList<>(); adapters.addAll(ADAPTERS_TO_CHECK); @@ -303,7 +311,29 @@ private void initialize() { adapters.add(new CustomAdapterPair(FIVE_PRIME_ADAPTER, THREE_PRIME_ADAPTER)); } - /** + if (USE_NEW_CONVERTER) { + final MetricsFile metrics = getMetricsFile(); + + if (METRICS_FILE != null) { + IOUtil.assertFileIsWritable(METRICS_FILE); + } else { + log.warn("No METRIC_FILE specified. Barcode metrics will not be generated."); + } + basecallsConverter = new NewIlluminaBasecallsConverter<>(BASECALLS_DIR, BARCODES_DIR, LANE, readStructure, + barcodeSamWriterMap, true, Math.max(1, MAX_READS_IN_RAM_PER_TILE / numOutputRecords), + TMP_DIR, NUM_PROCESSORS, + FIRST_TILE, TILE_LIMIT, new QueryNameComparator(), + new Codec(numOutputRecords), + SAMRecordsForCluster.class, bclQualityEvaluationStrategy, + this.APPLY_EAMSS_FILTER, INCLUDE_NON_PF_READS, IGNORE_UNEXPECTED_BARCODES, MAX_NO_CALLS, + MAX_MISMATCHES, MIN_MISMATCH_DELTA, MINIMUM_QUALITY, metrics, METRICS_FILE); + } else { + basecallsConverter = new IlluminaBasecallsConverter<>(BASECALLS_DIR, BARCODES_DIR, LANE, readStructure, + barcodeSamWriterMap, true, MAX_READS_IN_RAM_PER_TILE / numOutputRecords, TMP_DIR, NUM_PROCESSORS, FORCE_GC, + FIRST_TILE, TILE_LIMIT, new QueryNameComparator(), new Codec(numOutputRecords), SAMRecordsForCluster.class, + bclQualityEvaluationStrategy, this.APPLY_EAMSS_FILTER, INCLUDE_NON_PF_READS, IGNORE_UNEXPECTED_BARCODES); + } + /* * Be sure to pass the outputReadStructure to ClusterDataToSamConverter, which reflects the structure of the output cluster * data which may be different from the input read structure (specifically if there are skips). */ @@ -313,7 +343,7 @@ private void initialize() { .withMolecularIndexQualityTag(MOLECULAR_INDEX_BASE_QUALITY_TAG) .withTagPerMolecularIndex(TAG_PER_MOLECULAR_INDEX); basecallsConverter.setConverter(converter); - + log.info("DONE_READING STRUCTURE IS " + readStructure.toString()); } /** @@ -324,17 +354,17 @@ private void initialize() { * @return actualCols - expectedCols */ private Set findAndFilterExpectedColumns(final Set actualCols, final Set expectedCols) { - final Set missingColumns = new HashSet(expectedCols); + final Set missingColumns = new HashSet<>(expectedCols); missingColumns.removeAll(actualCols); if (!missingColumns.isEmpty()) { throw new PicardException(String.format( "LIBRARY_PARAMS file %s is missing the following columns: %s.", LIBRARY_PARAMS.getAbsolutePath(), StringUtil.join(", ", missingColumns - ))); + ))); } - final Set remainingColumns = new HashSet(actualCols); + final Set remainingColumns = new HashSet<>(actualCols); remainingColumns.removeAll(expectedCols); return remainingColumns; } @@ -369,7 +399,7 @@ private void populateWritersFromLibraryParams() { final TabbedTextFileWithHeaderParser libraryParamsParser = new TabbedTextFileWithHeaderParser(LIBRARY_PARAMS); final Set expectedColumnLabels = CollectionUtil.makeSet("OUTPUT", "SAMPLE_ALIAS", "LIBRARY_NAME"); - final List barcodeColumnLabels = new ArrayList(); + final List barcodeColumnLabels = new ArrayList<>(); if (readStructure.sampleBarcodes.length() == 1) { //For the single barcode read case, the barcode label name can either by BARCODE or BARCODE_1 if (libraryParamsParser.hasColumn("BARCODE")) { @@ -393,7 +423,7 @@ private void populateWritersFromLibraryParams() { List barcodeValues = null; if (!barcodeColumnLabels.isEmpty()) { - barcodeValues = new ArrayList(); + barcodeValues = new ArrayList<>(); for (final String barcodeLabel : barcodeColumnLabels) { barcodeValues.add(row.getField(barcodeLabel)); } @@ -412,7 +442,7 @@ private void populateWritersFromLibraryParams() { } final SAMFileWriterWrapper writer = buildSamFileWriter(new File(row.getField("OUTPUT")), - row.getField("SAMPLE_ALIAS"), row.getField("LIBRARY_NAME"), samHeaderParams); + row.getField("SAMPLE_ALIAS"), row.getField("LIBRARY_NAME"), samHeaderParams, !USE_NEW_CONVERTER); barcodeSamWriterMap.put(key, writer); } if (barcodeSamWriterMap.isEmpty()) { @@ -430,7 +460,7 @@ private void populateWritersFromLibraryParams() { * @return A Map of ReadGroupHeaderTags -> Values */ private Map buildSamHeaderParameters(final List barcodes) { - final Map params = new LinkedHashMap(); + final Map params = new LinkedHashMap<>(); String platformUnit = RUN_BARCODE + "." + LANE; if (barcodes != null) platformUnit += ("." + IlluminaUtil.barcodeSeqsToString(barcodes)); @@ -453,7 +483,8 @@ private void populateWritersFromLibraryParams() { * @return A SAMFileWriter */ private SAMFileWriterWrapper buildSamFileWriter(final File output, final String sampleAlias, - final String libraryName, final Map headerParameters) { + final String libraryName, final Map headerParameters, + final boolean presorted) { IOUtil.assertFileIsWritable(output); final SAMReadGroupRecord rg = new SAMReadGroupRecord(READ_GROUP_ID); rg.setSample(sampleAlias); @@ -469,7 +500,7 @@ private SAMFileWriterWrapper buildSamFileWriter(final File output, final String header.setSortOrder(SAMFileHeader.SortOrder.queryname); header.addReadGroup(rg); - return new SAMFileWriterWrapper(new SAMFileWriterFactory().makeSAMOrBAMWriter(header, true, output)); + return new SAMFileWriterWrapper(new SAMFileWriterFactory().makeSAMOrBAMWriter(header, presorted, output)); } public static void main(final String[] args) { @@ -482,7 +513,7 @@ public static void main(final String[] args) { * Any options set by command-line parser can be validated. * * @return null if command line is valid. If command line is invalid, returns an array of error message - * to be written to the appropriate place. + * to be written to the appropriate place. */ @Override protected String[] customCommandLineValidation() { @@ -490,7 +521,7 @@ public static void main(final String[] args) { LIBRARY_PARAMS = BARCODE_PARAMS; } - final ArrayList messages = new ArrayList(); + final ArrayList messages = new ArrayList<>(); readStructure = new ReadStructure(READ_STRUCTURE); if (!readStructure.sampleBarcodes.isEmpty() && LIBRARY_PARAMS == null) { @@ -517,7 +548,7 @@ public static void main(final String[] args) { } private static final class SAMFileWriterWrapper - implements IlluminaBasecallsConverter.ConvertedClusterDataWriter { + implements BasecallsConverter.ConvertedClusterDataWriter { public final SAMFileWriter writer; private SAMFileWriterWrapper(final SAMFileWriter writer) { @@ -547,6 +578,7 @@ public void close() { static class QueryNameComparator implements Comparator { private final SAMRecordQueryNameComparator comparator = new SAMRecordQueryNameComparator(); + @Override public int compare(final SAMRecordsForCluster s1, final SAMRecordsForCluster s2) { return comparator.compare(s1.records[0], s2.records[0]); diff --git a/src/main/java/picard/illumina/IlluminaPhasingMetrics.java b/src/main/java/picard/illumina/IlluminaPhasingMetrics.java index b56f26c46..56c939119 100644 --- a/src/main/java/picard/illumina/IlluminaPhasingMetrics.java +++ b/src/main/java/picard/illumina/IlluminaPhasingMetrics.java @@ -24,11 +24,11 @@ package picard.illumina; +import htsjdk.samtools.metrics.MetricBase; import picard.illumina.parser.Tile; import picard.illumina.parser.TileTemplateRead; -import htsjdk.samtools.metrics.MetricBase; -import java.lang.String;import java.util.ArrayList; +import java.util.ArrayList; import java.util.Collection; @@ -50,8 +50,8 @@ /** Median pre-phasing value across all tiles in a lane, applied to the first and second template reads */ public double PREPHASING_APPLIED; /** Calculate the median phasing & prephasing values for a lane's tiles and create the appropriate IlluminaPhasingMetrics for them */ - public static Collection getPhasingMetricsForTiles(final long lane, final Collection tilesForLane) { - final LanePhasingMetricsCollector lanePhasingMetricsCollector = new LanePhasingMetricsCollector(tilesForLane); + public static Collection getPhasingMetricsForTiles(final long lane, final Collection tilesForLane, boolean usePercentage) { + final LanePhasingMetricsCollector lanePhasingMetricsCollector = new LanePhasingMetricsCollector(tilesForLane, usePercentage); final Collection phasingMetrics = new ArrayList(); for (final TileTemplateRead tileTemplateRead : lanePhasingMetricsCollector.getMedianPhasingMap().keySet()) { final IlluminaPhasingMetrics phasingMetric = new IlluminaPhasingMetrics(); diff --git a/src/main/java/picard/illumina/LanePhasingMetricsCollector.java b/src/main/java/picard/illumina/LanePhasingMetricsCollector.java index 0f542ef95..c755933a9 100644 --- a/src/main/java/picard/illumina/LanePhasingMetricsCollector.java +++ b/src/main/java/picard/illumina/LanePhasingMetricsCollector.java @@ -24,12 +24,11 @@ package picard.illumina; +import htsjdk.samtools.util.CollectionUtil; import picard.illumina.parser.Tile; import picard.illumina.parser.TileTemplateRead; import picard.util.MathUtil; -import htsjdk.samtools.util.CollectionUtil; -import java.lang.Float; import java.util.Collection; import java.util.Collections; import java.util.Map; @@ -43,7 +42,7 @@ /** Constructor takes a lane's collection of Tiles and calculates the median phasing/prephasing for the * first and second (if available) reads */ - public LanePhasingMetricsCollector(final Collection laneTiles) { + public LanePhasingMetricsCollector(final Collection laneTiles, boolean usePercentage) { final Map medianPhasingMap = new TreeMap(); final Map medianPrePhasingMap = new TreeMap(); @@ -60,8 +59,8 @@ public LanePhasingMetricsCollector(final Collection laneTiles) { // Calculate the medians for the collected data for (final TileTemplateRead tileTemplateRead : phasingValues.keySet()) { - medianPhasingMap.put(tileTemplateRead, medianPercentage(phasingValues.get(tileTemplateRead))); - medianPrePhasingMap.put(tileTemplateRead, medianPercentage(prePhasingValues.get(tileTemplateRead))); + medianPhasingMap.put(tileTemplateRead, median(phasingValues.get(tileTemplateRead), usePercentage)); + medianPrePhasingMap.put(tileTemplateRead, median(prePhasingValues.get(tileTemplateRead), usePercentage)); } this.medianPhasingMap = Collections.unmodifiableMap(medianPhasingMap); @@ -76,13 +75,16 @@ public LanePhasingMetricsCollector(final Collection laneTiles) { return medianPrePhasingMap; } - private static float medianPercentage(final Collection phaseValues) { + + private static float median(final Collection phaseValues, boolean usePercentage) { final double[] values = new double[phaseValues.size()]; int i = 0; for (Float phaseValue : phaseValues) { values[i] = (double)phaseValue; i++; } - return (float)MathUtil.median(values) * 100; + float median = (float) MathUtil.median(values); + return usePercentage ? median * 100 : median; } + } diff --git a/src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java b/src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java new file mode 100644 index 000000000..708b710c0 --- /dev/null +++ b/src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java @@ -0,0 +1,395 @@ +package picard.illumina; + + +import htsjdk.samtools.metrics.MetricsFile; +import htsjdk.samtools.util.CloserUtil; +import htsjdk.samtools.util.IOUtil; +import htsjdk.samtools.util.Log; +import htsjdk.samtools.util.SortingCollection; +import htsjdk.samtools.util.StringUtil; +import picard.PicardException; +import picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric; +import picard.illumina.parser.BaseIlluminaDataProvider; +import picard.illumina.parser.ClusterData; +import picard.illumina.parser.IlluminaDataProviderFactory; +import picard.illumina.parser.IlluminaFileUtil; +import picard.illumina.parser.ParameterizedFileUtil; +import picard.illumina.parser.ReadDescriptor; +import picard.illumina.parser.ReadStructure; +import picard.illumina.parser.ReadType; +import picard.illumina.parser.readers.AbstractIlluminaPositionFileReader; +import picard.illumina.parser.readers.BclQualityEvaluationStrategy; +import picard.illumina.parser.readers.LocsFileReader; +import picard.util.IlluminaUtil; + +import java.io.File; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.Comparator; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.concurrent.CancellationException; +import java.util.concurrent.ExecutionException; +import java.util.concurrent.Future; +import java.util.concurrent.LinkedBlockingDeque; +import java.util.concurrent.ThreadPoolExecutor; +import java.util.concurrent.TimeUnit; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +public class NewIlluminaBasecallsConverter extends BasecallsConverter { + private static final Log log = Log.getInstance(NewIlluminaBasecallsConverter.class); + private final Map barcodesMetrics = new HashMap<>(); + private final BarcodeMetric noMatchMetric; + private final List cbcls; + private final List locs = new ArrayList<>(); + private final File[] filterFiles; + private final int maxNoCalls; + private final int maxMismatches; + private final int minMismatchDelta; + private final int minimumBaseQuality; + private final MetricsFile metrics; + private final File metricsFile; + private final Map barcodeWriterThreads = new HashMap<>(); + private final Map> completedWork = Collections.synchronizedMap(new HashMap<>()); + + /** + * @param basecallsDir Where to read basecalls from. + * @param barcodesDir Where to read barcodes from (optional; use basecallsDir if not specified). + * @param lane What lane to process. + * @param readStructure How to interpret each cluster. + * @param barcodeRecordWriterMap Map from barcode to CLUSTER_OUTPUT_RECORD writer. If demultiplex is false, must contain + * one writer stored with key=null. + * @param demultiplex If true, output is split by barcode, otherwise all are written to the same output stream. + * @param maxReadsInRamPerTile Configures number of reads each tile will store in RAM before spilling to disk. + * @param tmpDirs For SortingCollection spilling. + * @param numProcessors Controls number of threads. If <= 0, the number of threads allocated is + * available cores - numProcessors. + * @param firstTile (For debugging) If non-null, start processing at this tile. + * @param tileLimit (For debugging) If non-null, process no more than this many tiles. + * @param outputRecordComparator For sorting output records within a single tile. + * @param codecPrototype For spilling output records to disk. + * @param outputRecordClass Inconveniently needed to create SortingCollections. + * @param includeNonPfReads If true, will include ALL reads (including those which do not have PF set) + * @param ignoreUnexpectedBarcodes If true, will ignore reads whose called barcode is not found in barcodeRecordWriterMap, + * @param maxNoCalls The maximum number of no calls to allow in a match. + * @param maxMismatches The maximum number of mismatched calls to allow in a match. + * @param minMismatchDelta The minimum mismatch difference between the best and second best matches. + * @param minimumBaseQuality The minimum base quality to allow for a matching base call. + * @param metrics The metrics output for barcode metrics. + * @param metricsFile The metrics file to write out the barcode metrics to. + */ + public NewIlluminaBasecallsConverter(final File basecallsDir, File barcodesDir, final int lane, + final ReadStructure readStructure, + final Map> barcodeRecordWriterMap, + final boolean demultiplex, + final int maxReadsInRamPerTile, + final List tmpDirs, final int numProcessors, + final Integer firstTile, + final Integer tileLimit, + final Comparator outputRecordComparator, + final SortingCollection.Codec codecPrototype, + final Class outputRecordClass, + final BclQualityEvaluationStrategy bclQualityEvaluationStrategy, + final boolean applyEamssFiltering, final boolean includeNonPfReads, + final boolean ignoreUnexpectedBarcodes, int maxNoCalls, int maxMismatches, + int minMismatchDelta, int minimumBaseQuality, MetricsFile metrics, File metricsFile) { + + super(barcodeRecordWriterMap, maxReadsInRamPerTile, tmpDirs, codecPrototype, ignoreUnexpectedBarcodes, + demultiplex, outputRecordComparator, includeNonPfReads, bclQualityEvaluationStrategy, + outputRecordClass, numProcessors, new IlluminaDataProviderFactory(basecallsDir, + barcodesDir, lane, readStructure, bclQualityEvaluationStrategy)); + this.maxNoCalls = maxNoCalls; + this.maxMismatches = maxMismatches; + this.minMismatchDelta = minMismatchDelta; + this.minimumBaseQuality = minimumBaseQuality; + this.tiles = new ArrayList<>(); + this.metrics = metrics; + this.metricsFile = metricsFile; + int numBarcodes = readStructure.sampleBarcodes.length(); + + barcodeRecordWriterMap.keySet().forEach(barcode -> { + if (barcode != null) { + int pos = 0; + String[] bcStrings = new String[numBarcodes]; + for (int i = 0; i < numBarcodes; i++) { + int endIndex = readStructure.sampleBarcodes.getDescriptorLengths()[i]; + bcStrings[i] = barcode.substring(pos, endIndex + pos); + pos += endIndex; + } + this.barcodesMetrics.put(barcode, new BarcodeMetric(null, null, barcode, bcStrings)); + } + barcodeWriterThreads.put(barcode, new ThreadPoolExecutorWithExceptions(1)); + }); + + File laneDir = new File(basecallsDir, IlluminaFileUtil.longLaneStr(lane)); + + File[] cycleDirs = IOUtil.getFilesMatchingRegexp(laneDir, IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN); + + //CBCLs + cbcls = new ArrayList<>(); + Arrays.asList(cycleDirs) + .forEach(cycleDir -> cbcls.addAll( + Arrays.asList(IOUtil.getFilesMatchingRegexp( + cycleDir, "^" + IlluminaFileUtil.longLaneStr(lane) + "_(\\d{1,5}).cbcl$")))); + + if (cbcls.size() == 0) { + throw new PicardException("No CBCL files found."); + } + + IOUtil.assertFilesAreReadable(cbcls); + + //locs + File locsFile = new File(basecallsDir.getParentFile(), "s.locs"); + try (LocsFileReader locsFileReader = new LocsFileReader(locsFile)) { + while (locsFileReader.hasNext()) { + locs.add(locsFileReader.next()); + } + } + IOUtil.assertFileIsReadable(locsFile); + //filter + + Pattern laneTileRegex = Pattern.compile(ParameterizedFileUtil.escapePeriods( + ParameterizedFileUtil.makeLaneTileRegex(".filter", lane))); + filterFiles = getTiledFiles(laneDir, laneTileRegex); + for (File filterFile : filterFiles) { + Matcher tileMatcher = laneTileRegex.matcher(filterFile.getName()); + if (tileMatcher.matches()) { + tiles.add(Integer.valueOf(tileMatcher.group(1))); + } + } + IOUtil.assertFilesAreReadable(Arrays.asList(filterFiles)); + tiles.sort(TILE_NUMBER_COMPARATOR); + + this.factory.setApplyEamssFiltering(applyEamssFiltering); + setTileLimits(firstTile, tileLimit); + + // Create BarcodeMetric for counting reads that don't match any barcode + final String[] noMatchBarcode = new String[readStructure.sampleBarcodes.length()]; + int index = 0; + for (final ReadDescriptor d : readStructure.descriptors) { + if (d.type == ReadType.Barcode) { + noMatchBarcode[index++] = StringUtil.repeatCharNTimes('N', d.length); + } + } + + this.noMatchMetric = new BarcodeMetric(null, null, IlluminaUtil.barcodeSeqsToString(noMatchBarcode), noMatchBarcode); + + } + + public static File[] getTiledFiles(File baseDirectory, Pattern pattern) { + return IOUtil.getFilesMatchingRegexp(baseDirectory, pattern); + } + + @Override + public void doTileProcessing() { + + ThreadPoolExecutor completedWorkExecutor = new ThreadPoolExecutorWithExceptions(1); + + CompletedWorkChecker workChecker = new CompletedWorkChecker(); + completedWorkExecutor.submit(workChecker); + completedWorkExecutor.shutdown(); + + //thread by surface tile + ThreadPoolExecutor tileProcessingExecutor = new ThreadPoolExecutorWithExceptions(numThreads); + + for (Integer tile : tiles) { + tileProcessingExecutor.submit(new TileProcessor(tile)); + } + + tileProcessingExecutor.shutdown(); + + awaitThreadPoolTermination("Reading executor", tileProcessingExecutor); + awaitThreadPoolTermination("Tile completion executor", completedWorkExecutor); + + barcodeWriterThreads.values().forEach(ThreadPoolExecutor::shutdown); + barcodeWriterThreads.forEach((barcode, executor) -> awaitThreadPoolTermination(barcode + " writer", executor)); + + if (metricsFile != null) { + ExtractIlluminaBarcodes.finalizeMetrics(barcodesMetrics, noMatchMetric); + + for (final BarcodeMetric barcodeMetric : barcodesMetrics.values()) { + metrics.addMetric(barcodeMetric); + } + metrics.addMetric(noMatchMetric); + metrics.write(metricsFile); + CloserUtil.close(metricsFile); + } + } + + private void awaitThreadPoolTermination(String executorName, ThreadPoolExecutor executorService) { + try { + while (!executorService.awaitTermination(300, TimeUnit.SECONDS)) { + log.info(String.format("%s waiting for job completion. Finished jobs - %d : Running jobs - %d : Queued jobs - %d", + executorName, executorService.getCompletedTaskCount(), executorService.getActiveCount(), + executorService.getQueue().size())); + } + } catch (InterruptedException e) { + e.printStackTrace(); + } + } + + private class RecordWriter implements Runnable { + private final SortingCollection recordCollection; + private final ConvertedClusterDataWriter writer; + private final String barcode; + + RecordWriter(ConvertedClusterDataWriter writer, + SortingCollection recordCollection, String barcode) { + this.writer = writer; + this.recordCollection = recordCollection; + this.barcode = barcode; + } + + @Override + public void run() { + for (CLUSTER_OUTPUT_RECORD record : recordCollection) { + writer.write(record); + writeProgressLogger.record(null, 0); + } + } + + public String getBarcode() { + return barcode; + } + } + + private class Closer implements Runnable { + private final ConvertedClusterDataWriter writer; + private final String barcode; + + private Closer(ConvertedClusterDataWriter writer, String barcode) { + this.writer = writer; + this.barcode = barcode; + } + + @Override + public void run() { + log.info("Closing writer for barcode " + barcode); + this.writer.close(); + } + } + + private class TileProcessor implements Runnable { + private final int tileNum; + private final Map> barcodeToRecordCollection = new HashMap<>(); + + TileProcessor(int tileNum) { + this.tileNum = tileNum; + } + + @Override + public void run() { + final BaseIlluminaDataProvider dataProvider = factory.makeDataProvider(cbcls, locs, filterFiles, tileNum, barcodesMetrics, + noMatchMetric, maxNoCalls, maxMismatches, minMismatchDelta, minimumBaseQuality); + + while (dataProvider.hasNext()) { + final ClusterData cluster = dataProvider.next(); + readProgressLogger.record(null, 0); + final String barcode = (demultiplex ? cluster.getMatchedBarcode() : null); + addRecord(barcode, converter.convertClusterToOutputRecord(cluster)); + } + + dataProvider.close(); + + List writerList = new ArrayList<>(); + barcodeToRecordCollection.forEach((barcode, value) -> { + value.doneAdding(); + ConvertedClusterDataWriter writer = barcodeRecordWriterMap.get(barcode); + writerList.add(new RecordWriter(writer, value, barcode)); + + }); + completedWork.put(tileNum, writerList); + + log.info("Finished processing tile " + tileNum); + } + + private synchronized void addRecord(final String barcode, final CLUSTER_OUTPUT_RECORD record) { + // Grab the existing collection, or initialize it if it doesn't yet exist + SortingCollection recordCollection = this.barcodeToRecordCollection.get(barcode); + if (recordCollection == null) { + // TODO: The implementation here for supporting ignoreUnexpectedBarcodes is not efficient, + // but the alternative is an extensive rewrite. We are living with the inefficiency for + // this special case for the time being. + if (!barcodeRecordWriterMap.containsKey(barcode)) { + if (ignoreUnexpectedBarcodes) { + return; + } + throw new PicardException(String.format("Read records with barcode %s, but this barcode was not expected. (Is it referenced in the parameters file?)", barcode)); + } + recordCollection = newSortingCollection(); + this.barcodeToRecordCollection.put(barcode, recordCollection); + } + recordCollection.add(record); + } + + private synchronized SortingCollection newSortingCollection() { + final int maxRecordsInRam = + Math.max(1, maxReadsInRamPerTile / + barcodeRecordWriterMap.size()); + return SortingCollection.newInstance( + outputRecordClass, + codecPrototype.clone(), + outputRecordComparator, + maxRecordsInRam, + tmpDirs); + } + } + + private class ThreadPoolExecutorWithExceptions extends ThreadPoolExecutor { + ThreadPoolExecutorWithExceptions(int threads) { + super(threads, threads, 0, TimeUnit.SECONDS, new LinkedBlockingDeque<>()); + } + + @Override + protected void afterExecute(Runnable r, Throwable t) { + if (t == null && r instanceof Future) { + try { + Future future = (Future) r; + if (future.isDone()) { + future.get(); + } + } catch (CancellationException ce) { + t = ce; + } catch (ExecutionException ee) { + t = ee.getCause(); + } catch (InterruptedException ie) { + Thread.currentThread().interrupt(); // ignore/reset + } + } + if (t != null) { + throw new PicardException(t.getMessage(), t); + } + } + } + + + private class CompletedWorkChecker implements Runnable { + + private int currentTileIndex = 0; + + @Override + public void run() { + while (currentTileIndex < tiles.size()) { + Integer currentTile = tiles.get(currentTileIndex); + if (completedWork.containsKey(currentTile)) { + log.info("Writing out tile " + currentTile); + completedWork.get(currentTile).forEach(writer -> barcodeWriterThreads.get(writer.getBarcode()).submit(writer)); + currentTileIndex++; + } else { + try { + Thread.sleep(5000); + } catch (InterruptedException e) { + throw new PicardException(e.getMessage(), e); + } + } + } + + //we are all done scheduling work.. now schedule the closes + barcodeRecordWriterMap.forEach((barcode, writer) -> barcodeWriterThreads.get(barcode).submit(new Closer(writer, barcode))); + } + + } +} diff --git a/src/main/java/picard/illumina/parser/BaseIlluminaDataProvider.java b/src/main/java/picard/illumina/parser/BaseIlluminaDataProvider.java new file mode 100644 index 000000000..d405ec53f --- /dev/null +++ b/src/main/java/picard/illumina/parser/BaseIlluminaDataProvider.java @@ -0,0 +1,81 @@ +package picard.illumina.parser; + +import java.util.Iterator; +import java.util.stream.StreamSupport; + +/** + * Parse various formats and versions of Illumina Basecall files, and use them the to populate + * ClusterData objects. + */ +public abstract class BaseIlluminaDataProvider implements Iterator, Iterable, AutoCloseable { + + protected final int lane; + /** + * Calculated once, outputReadTypes describes the type of read data for each ReadData that will be found in output ClusterData objects + */ + final ReadType[] outputReadTypes; + /** + * Number of reads in each ClusterData + */ + final int numReads; + + public BaseIlluminaDataProvider(final int lane, final OutputMapping outputMapping) { + numReads = outputMapping.numOutputReads(); + this.lane = lane; + this.outputReadTypes = StreamSupport.stream(outputMapping.getOutputDescriptors().spliterator(), false) + .map(rd -> rd.type).toArray(ReadType[]::new); + } + + @Override + public Iterator iterator() { + return this; + } + + public abstract void close(); + + /* + * Methods for that transfer data from the IlluminaData objects to the current cluster + */ + protected void addData(final ClusterData clusterData, final PositionalData posData) { + clusterData.setX(posData.getXCoordinate()); + clusterData.setY(posData.getYCoordinate()); + } + + protected void addData(final ClusterData clusterData, final PfData pfData) { + clusterData.setPf(pfData.isPf()); + } + + protected void addData(final ClusterData clusterData, final BarcodeData barcodeData) { + clusterData.setMatchedBarcode(barcodeData.getBarcode()); + } + + protected void addReadData(final ClusterData clusterData, final int numReads, final BaseData baseData) { + final byte[][] bases = baseData.getBases(); + for (int i = 0; i < numReads; i++) { + clusterData.getRead(i).setBases(bases[i]); + } + } + + protected void addReadData(final ClusterData clusterData, final int numReads, final QualityData qualityData) { + final byte[][] qualities = qualityData.getQualities(); + for (int i = 0; i < numReads; i++) { + clusterData.getRead(i).setQualities(qualities[i]); + } + } + + protected void addReadData(final ClusterData clusterData, final int numReads, final CbclData cbclData) { + final byte[][] bases = cbclData.getBases(); + for (int i = 0; i < numReads; i++) { + clusterData.getRead(i).setBases(bases[i]); + } + final byte[][] qualities = cbclData.getQualities(); + for (int i = 0; i < numReads; i++) { + clusterData.getRead(i).setQualities(qualities[i]); + } + clusterData.setPf(cbclData.isPf()); + clusterData.setX(cbclData.getPositionInfo().xQseqCoord); + clusterData.setY(cbclData.getPositionInfo().yQseqCoord); + } + + abstract void seekToTile(int seekAfterFirstRead); +} diff --git a/src/main/java/picard/illumina/parser/CbclData.java b/src/main/java/picard/illumina/parser/CbclData.java new file mode 100644 index 000000000..ca1601757 --- /dev/null +++ b/src/main/java/picard/illumina/parser/CbclData.java @@ -0,0 +1,45 @@ +package picard.illumina.parser; + +import picard.illumina.parser.readers.AbstractIlluminaPositionFileReader; + +/** + * This class provides that data structure for cbcls. This includes BCL data as well as PF (pass-filter) data and + * positional information. + */ +public class CbclData extends BclData implements PfData, PositionalData { + private final int tile; + private AbstractIlluminaPositionFileReader.PositionInfo positionInfo; + + public CbclData(int[] outputLengths, int tile) { + super(outputLengths); + this.tile = tile; + } + + //CBCLs currently only contain PF reads. + @Override + public boolean isPf() { + return true; + } + + public int getTile() { + return tile; + } + + public AbstractIlluminaPositionFileReader.PositionInfo getPositionInfo() { + return positionInfo; + } + + public void setPositionInfo(AbstractIlluminaPositionFileReader.PositionInfo positionInfo) { + this.positionInfo = positionInfo; + } + + @Override + public int getXCoordinate() { + return this.positionInfo.xQseqCoord; + } + + @Override + public int getYCoordinate() { + return this.positionInfo.yQseqCoord; + } +} diff --git a/src/main/java/picard/illumina/parser/IlluminaDataProvider.java b/src/main/java/picard/illumina/parser/IlluminaDataProvider.java index fc3a327b7..618884370 100644 --- a/src/main/java/picard/illumina/parser/IlluminaDataProvider.java +++ b/src/main/java/picard/illumina/parser/IlluminaDataProvider.java @@ -27,7 +27,6 @@ import picard.PicardException; import java.io.File; -import java.util.Iterator; import java.util.Map; import java.util.NoSuchElementException; import java.util.Set; @@ -39,13 +38,16 @@ * * @author jburke@broadinstitute.org */ -public class IlluminaDataProvider implements Iterator, Iterable { +public class IlluminaDataProvider extends BaseIlluminaDataProvider { - /** contains QSeqs, bcls, or other Illumina file types that will be parsed by this class */ + /** + * contains QSeqs, bcls, or other Illumina file types that will be parsed by this class + */ private final File basecallDirectory; //These two are for error reporting only - private final int lane; - /** A list of parsers (already initialized) that should output data in a format consistent with readStructure */ + /** + * A list of parsers (already initialized) that should output data in a format consistent with readStructure + */ private final IlluminaParser[] parsers; /** @@ -55,12 +57,6 @@ */ private final IlluminaDataType[][] dataTypes; - /** Calculated once, outputReadTypes describes the type of read data for each ReadData that will be found in output ClusterData objects */ - private final ReadType[] outputReadTypes; - - /** Number of reads in each ClusterData */ - private final int numReads; - /** * Create an IlluminaDataProvider given a map of parsersToDataTypes for particular file formats. Compute once the miscellaneous data for the * run that will be passed to each ClusterData. @@ -71,9 +67,8 @@ IlluminaDataProvider(final OutputMapping outputMapping, final Map> parsersToDataTypes, final File basecallDirectory, final int lane) { + super(lane, outputMapping); this.basecallDirectory = basecallDirectory; - this.lane = lane; - numReads = outputMapping.numOutputReads(); final int numParsers = parsersToDataTypes.size(); if (numParsers == 0) { @@ -90,11 +85,6 @@ dts.toArray(dataTypes[i++]); } - this.outputReadTypes = new ReadType[numReads]; - i = 0; - for (final ReadDescriptor rd : outputMapping.getOutputDescriptors()) { - outputReadTypes[i++] = rd.type; - } } /** @@ -162,55 +152,14 @@ public ClusterData next() { return cluster; } - /* - * Methods for that transfer data from the IlluminaData objects to the current cluster - */ - private void addData(final ClusterData clusterData, final PositionalData posData) { - clusterData.setX(posData.getXCoordinate()); - clusterData.setY(posData.getYCoordinate()); - } - - private void addData(final ClusterData clusterData, final PfData pfData) { - clusterData.setPf(pfData.isPf()); - } - - private void addData(final ClusterData clusterData, final BarcodeData barcodeData) { - clusterData.setMatchedBarcode(barcodeData.getBarcode()); - } - - private void addReadData(final ClusterData clusterData, final int numReads, final BaseData baseData) { - final byte[][] bases = baseData.getBases(); - for (int i = 0; i < numReads; i++) { - clusterData.getRead(i).setBases(bases[i]); - } - } - - private void addReadData(final ClusterData clusterData, final int numReads, final QualityData qualityData) { - final byte[][] qualities = qualityData.getQualities(); - for (int i = 0; i < numReads; i++) { - clusterData.getRead(i).setQualities(qualities[i]); - } - } - - private void addReadData(final ClusterData clusterData, final int numReads, final RawIntensityData rawIntensityData) { - final FourChannelIntensityData[] fcids = rawIntensityData.getRawIntensities(); - for (int i = 0; i < numReads; i++) { - clusterData.getRead(i).setRawIntensities(fcids[i]); - } - } - - private void addReadData(final ClusterData clusterData, final int numReads, final NoiseData noiseData) { - final FourChannelIntensityData[] fcids = noiseData.getNoise(); - for (int i = 0; i < numReads; i++) { - clusterData.getRead(i).setNoise(fcids[i]); - } - } - public void remove() { throw new UnsupportedOperationException(); } - /** Jump so that the next record returned will be from the specified tile. */ + /** + * Jump so that the next record returned will be from the specified tile. + */ + @Override public void seekToTile(final int oneBasedTileNumber) { for (final IlluminaParser parser : parsers) { parser.seekToTile(oneBasedTileNumber); @@ -218,10 +167,6 @@ public void seekToTile(final int oneBasedTileNumber) { } @Override - public Iterator iterator() { - return this; - } - public void close() { for (final IlluminaParser parser : parsers) { parser.close(); diff --git a/src/main/java/picard/illumina/parser/IlluminaDataProviderFactory.java b/src/main/java/picard/illumina/parser/IlluminaDataProviderFactory.java index 9842d75db..2b834c34f 100644 --- a/src/main/java/picard/illumina/parser/IlluminaDataProviderFactory.java +++ b/src/main/java/picard/illumina/parser/IlluminaDataProviderFactory.java @@ -27,7 +27,9 @@ import htsjdk.samtools.util.Log; import htsjdk.samtools.util.StringUtil; import picard.PicardException; +import picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric; import picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat; +import picard.illumina.parser.readers.AbstractIlluminaPositionFileReader; import picard.illumina.parser.readers.BclQualityEvaluationStrategy; import java.io.File; @@ -68,10 +70,10 @@ * We try to prefer data types that will be the fastest to parse/smallest in memory * NOTE: In the code below, if Qseq is chosen to provide for ANY data type then it is used for ALL its data types (since we'll have to parse the entire line for each Qseq anyways) */ - private static final Map> DATA_TYPE_TO_PREFERRED_FORMATS = new EnumMap>(IlluminaDataType.class); + private static final Map> DATA_TYPE_TO_PREFERRED_FORMATS = new EnumMap<>(IlluminaDataType.class); static { - /** For types found in Qseq, we prefer the NON-Qseq file formats first. However, if we end up using Qseqs then we use Qseqs for EVERY type it provides, + /* For types found in Qseq, we prefer the NON-Qseq file formats first. However, if we end up using Qseqs then we use Qseqs for EVERY type it provides, * see determineFormats */ DATA_TYPE_TO_PREFERRED_FORMATS.put(IlluminaDataType.BaseCalls, makeList( @@ -88,7 +90,9 @@ } // The following properties must be specified by caller. - /** basecallDirectory holds QSeqs or bcls * */ + /** + * basecallDirectory holds QSeqs or bcls * + */ private final File basecallDirectory; private final File barcodesDirectory; private final int lane; @@ -103,7 +107,9 @@ */ protected final Map> formatToDataTypes; - /** Basecall Directory/lane parameterized util for finding IlluminaFiles */ + /** + * Basecall Directory/lane parameterized util for finding IlluminaFiles + */ private final IlluminaFileUtil fileUtil; @@ -113,25 +119,25 @@ private final BclQualityEvaluationStrategy bclQualityEvaluationStrategy; /** - * Create factory with the specified options, one that favors using QSeqs over all other files - * - * @param basecallDirectory The baseCalls directory of a complete Illumina directory. Files are found by searching relative to this folder (some of them higher up in the directory tree). - * @param lane Which lane to iterate over. - * @param readStructure The read structure to which output clusters will conform. When not using QSeqs, EAMSS masking(see BclParser) is run on individual reads as found in the readStructure, if - * the readStructure specified does not match the readStructure implied by the sequencer's output than the quality scores output may differ than what would be found - * in a run's QSeq files - * @param dataTypesArg Which data types to read - */ - public IlluminaDataProviderFactory(final File basecallDirectory, final int lane, final ReadStructure readStructure, - final BclQualityEvaluationStrategy bclQualityEvaluationStrategy, - final IlluminaDataType... dataTypesArg) { - this(basecallDirectory, null, - lane, readStructure, - bclQualityEvaluationStrategy, - dataTypesArg); - } - - /** + * Create factory with the specified options, one that favors using QSeqs over all other files + * + * @param basecallDirectory The baseCalls directory of a complete Illumina directory. Files are found by searching relative to this folder (some of them higher up in the directory tree). + * @param lane Which lane to iterate over. + * @param readStructure The read structure to which output clusters will conform. When not using QSeqs, EAMSS masking(see BclParser) is run on individual reads as found in the readStructure, if + * the readStructure specified does not match the readStructure implied by the sequencer's output than the quality scores output may differ than what would be found + * in a run's QSeq files + * @param dataTypesArg Which data types to read + */ + public IlluminaDataProviderFactory(final File basecallDirectory, final int lane, final ReadStructure readStructure, + final BclQualityEvaluationStrategy bclQualityEvaluationStrategy, + final IlluminaDataType... dataTypesArg) { + this(basecallDirectory, null, + lane, readStructure, + bclQualityEvaluationStrategy, + dataTypesArg); + } + + /** * Create factory with the specified options, one that favors using QSeqs over all other files * * @param basecallDirectory The baseCalls directory of a complete Illumina directory. Files are found by searching relative to this folder (some of them higher up in the directory tree). @@ -155,7 +161,7 @@ public IlluminaDataProviderFactory(final File basecallDirectory, File barcodesDi Note: In previous version, data of types not specified might be returned if a data type was specified for data residing in QSeqs (since QSeqs span multiple data types). This is no longer the case, you MUST specify all data types that should be returned.*/ - final Set dataTypes = Collections.unmodifiableSet(new HashSet(Arrays.asList(dataTypesArg))); + final Set dataTypes = Collections.unmodifiableSet(new HashSet<>(Arrays.asList(dataTypesArg))); if (dataTypes.isEmpty()) { throw new PicardException("No data types have been specified for basecall output " + basecallDirectory + @@ -170,12 +176,12 @@ public IlluminaDataProviderFactory(final File basecallDirectory, File barcodesDi //find if we have any IlluminaDataType with NO available file formats and, if any exist, throw an exception final Set unmatchedDataTypes = findUnmatchedTypes(dataTypes, formatToDataTypes); if (!unmatchedDataTypes.isEmpty()) { - throw new PicardException("Could not find a format with available files for the following data types: " + StringUtil.join(", ", new ArrayList(unmatchedDataTypes))); + throw new PicardException("Could not find a format with available files for the following data types: " + StringUtil.join(", ", new ArrayList<>(unmatchedDataTypes))); } log.debug("The following file formats will be used by IlluminaDataProvider: " + StringUtil.join("," + formatToDataTypes.keySet())); - availableTiles = fileUtil.getActualTiles(new ArrayList(formatToDataTypes.keySet())); + availableTiles = fileUtil.getActualTiles(new ArrayList<>(formatToDataTypes.keySet())); if (availableTiles.isEmpty()) { throw new PicardException("No available tiles were found, make sure that " + basecallDirectory.getAbsolutePath() + " has a lane " + lane); } @@ -183,6 +189,21 @@ public IlluminaDataProviderFactory(final File basecallDirectory, File barcodesDi outputMapping = new OutputMapping(readStructure); } + public IlluminaDataProviderFactory(File basecallDirectory, File barcodesDirectory, int lane, + ReadStructure readStructure, + BclQualityEvaluationStrategy bclQualityEvaluationStrategy) { + this.basecallDirectory = basecallDirectory; + this.barcodesDirectory = barcodesDirectory; + this.bclQualityEvaluationStrategy = bclQualityEvaluationStrategy; + + this.lane = lane; + + this.formatToDataTypes = null; + this.availableTiles = null; + this.fileUtil = null; + outputMapping = new OutputMapping(readStructure); + } + /** * Sometimes (in the case of skipped reads) the logical read structure of the output cluster data is different from the input * readStructure @@ -202,17 +223,36 @@ public ReadStructure getOutputReadStructure() { return availableTiles; } - /** Sets whether or not EAMSS filtering will be applied if parsing BCL files for bases and quality scores. */ + /** + * Sets whether or not EAMSS filtering will be applied if parsing BCL files for bases and quality scores. + */ public void setApplyEamssFiltering(final boolean applyEamssFiltering) { this.applyEamssFiltering = applyEamssFiltering; } /** - * Call this method to create a ClusterData iterator over all clusters for all tiles in ascending numeric order. + * Call this method to create a ClusterData iterator over all clusters for a given tile. * + * @param cbcls A list of cbcls to use when creating this data provider. + * @param filterFiles A list of the pf filter files to use when creating this data provider. + * @param barcodesMetrics A map of barcode to barcode metrics to output for this data provider. + * @param maxNoCalls The maximum number of no calls to allow in a match. + * @param maxMismatches The maximum number of mismatched calls to allow in a match. + * @param minMismatchDelta The minimum mismatch difference between the best and second best matches. + * @param minimumBaseQuality The minimum base quality to allow for a matching base call. * @return An iterator for reading the Illumina basecall output for the lane specified in the ctor. */ - public IlluminaDataProvider makeDataProvider() { + public NewIlluminaDataProvider makeDataProvider(List cbcls, + List locs, + File[] filterFiles, int tileNum, Map barcodesMetrics, + BarcodeMetric noMatchMetric, + int maxNoCalls, int maxMismatches, int minMismatchDelta, + int minimumBaseQuality) { + return new NewIlluminaDataProvider(cbcls, locs, filterFiles, lane, tileNum, outputMapping, + false, barcodesMetrics, noMatchMetric, maxNoCalls, maxMismatches, minMismatchDelta, minimumBaseQuality); + } + + public BaseIlluminaDataProvider makeDataProvider() { return makeDataProvider(null); } @@ -221,7 +261,7 @@ public IlluminaDataProvider makeDataProvider() { * * @return An iterator for reading the Illumina basecall output for the lane specified in the constructor. */ - public IlluminaDataProvider makeDataProvider(List requestedTiles) { + public BaseIlluminaDataProvider makeDataProvider(List requestedTiles) { if (requestedTiles == null) { requestedTiles = availableTiles; } else { @@ -230,7 +270,7 @@ public IlluminaDataProvider makeDataProvider(List requestedTiles) { } } - final Map> parsersToDataType = new HashMap>(); + final Map> parsersToDataType = new HashMap<>(); for (final Map.Entry> fmToDt : formatToDataTypes.entrySet()) { parsersToDataType.put(makeParser(fmToDt.getKey(), requestedTiles), fmToDt.getValue()); } @@ -248,7 +288,7 @@ public IlluminaDataProvider makeDataProvider(List requestedTiles) { * @return The data types that go unsupported by the formats found in formatToMatchedTypes */ public static Set findUnmatchedTypes(final Set requestedDataTypes, final Map> formatToMatchedTypes) { - final Set copiedTypes = new HashSet(requestedDataTypes); + final Set copiedTypes = new HashSet<>(requestedDataTypes); for (final Set matchedTypes : formatToMatchedTypes.values()) { copiedTypes.removeAll(matchedTypes); } @@ -266,9 +306,9 @@ public IlluminaDataProvider makeDataProvider(List requestedTiles) { */ public static Map> determineFormats(final Set requestedDataTypes, final IlluminaFileUtil fileUtil) { //For predictable ordering and uniqueness only, put the requestedDataTypes into a treeSet - final SortedSet toSupport = new TreeSet(requestedDataTypes); - final Map> fileTypeToDataTypes = new EnumMap>(SupportedIlluminaFormat.class); - final Map dataTypeToFormat = new EnumMap(IlluminaDataType.class); + final SortedSet toSupport = new TreeSet<>(requestedDataTypes); + final Map> fileTypeToDataTypes = new EnumMap<>(SupportedIlluminaFormat.class); + final Map dataTypeToFormat = new EnumMap<>(IlluminaDataType.class); for (final IlluminaDataType ts : toSupport) { final SupportedIlluminaFormat preferredFormat = findPreferredAvailableFormat(ts, fileUtil); @@ -341,11 +381,11 @@ private IlluminaParser makeParser(final SupportedIlluminaFormat format, final Li final IlluminaParser parser; switch (format) { case Barcode: - parser = new BarcodeParser(((PerTileFileUtil)fileUtil.getUtil(SupportedIlluminaFormat.Barcode)).getFiles(requestedTiles)); + parser = new BarcodeParser(((PerTileFileUtil) fileUtil.getUtil(SupportedIlluminaFormat.Barcode)).getFiles(requestedTiles)); break; case Bcl: { - final CycleIlluminaFileMap bclFileMap = ((PerTilePerCycleFileUtil)fileUtil.getUtil(SupportedIlluminaFormat.Bcl)) + final CycleIlluminaFileMap bclFileMap = ((PerTilePerCycleFileUtil) fileUtil.getUtil(SupportedIlluminaFormat.Bcl)) .getFiles(requestedTiles, outputMapping.getOutputCycles()); bclFileMap.assertValid(requestedTiles, outputMapping.getOutputCycles()); parser = new BclParser(basecallDirectory, lane, bclFileMap, outputMapping, this.applyEamssFiltering, bclQualityEvaluationStrategy); @@ -353,7 +393,7 @@ private IlluminaParser makeParser(final SupportedIlluminaFormat format, final Li } case Filter: - final IlluminaFileMap filterFileMap = ((PerTileFileUtil)fileUtil.getUtil(SupportedIlluminaFormat.Filter)).getFiles(requestedTiles); + final IlluminaFileMap filterFileMap = ((PerTileFileUtil) fileUtil.getUtil(SupportedIlluminaFormat.Filter)).getFiles(requestedTiles); parser = new FilterParser(filterFileMap); break; @@ -365,11 +405,11 @@ private IlluminaParser makeParser(final SupportedIlluminaFormat format, final Li break; case MultiTileFilter: - parser = ((MultiTileFilterFileUtil)fileUtil.getUtil(SupportedIlluminaFormat.MultiTileFilter)).makeParser(requestedTiles); + parser = ((MultiTileFilterFileUtil) fileUtil.getUtil(SupportedIlluminaFormat.MultiTileFilter)).makeParser(requestedTiles); break; case MultiTileLocs: - parser = ((MultiTileLocsFileUtil)fileUtil.getUtil(SupportedIlluminaFormat.MultiTileLocs)).makeParser(requestedTiles); + parser = ((MultiTileLocsFileUtil) fileUtil.getUtil(SupportedIlluminaFormat.MultiTileLocs)).makeParser(requestedTiles); break; case MultiTileBcl: { diff --git a/src/main/java/picard/illumina/parser/IlluminaFileUtil.java b/src/main/java/picard/illumina/parser/IlluminaFileUtil.java index 736054792..4fd65def0 100644 --- a/src/main/java/picard/illumina/parser/IlluminaFileUtil.java +++ b/src/main/java/picard/illumina/parser/IlluminaFileUtil.java @@ -170,7 +170,7 @@ public ParameterizedFileUtil getUtil(final SupportedIlluminaFormat format) { //Used just to ensure predictable ordering final TreeSet expectedTiles = new TreeSet(); - final Iterator tileMetrics = new TileMetricsOutReader(tileMetricsOut); + final Iterator tileMetrics = new TileMetricsOutReader(tileMetricsOut, TileMetricsOutReader.TileMetricsVersion.TWO); while (tileMetrics.hasNext()) { final TileMetricsOutReader.IlluminaTileMetrics tileMetric = tileMetrics.next(); diff --git a/src/main/java/picard/illumina/parser/NewIlluminaDataProvider.java b/src/main/java/picard/illumina/parser/NewIlluminaDataProvider.java new file mode 100644 index 000000000..d7d7c41c3 --- /dev/null +++ b/src/main/java/picard/illumina/parser/NewIlluminaDataProvider.java @@ -0,0 +1,118 @@ +package picard.illumina.parser; + +import picard.illumina.ExtractIlluminaBarcodes; +import picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric; +import picard.illumina.parser.readers.AbstractIlluminaPositionFileReader; +import picard.illumina.parser.readers.CbclReader; + +import java.io.File; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +import static picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor.findBestBarcodeAndUpdateMetrics; + +/** + * Parse cbcls Illumina Basecall files, and use them the to populate + * ClusterData objects. + */ +public class NewIlluminaDataProvider extends BaseIlluminaDataProvider { + private final CbclReader reader; + private final ReadStructure outputReadStructure; + private final boolean usingQualityScores; + private final Map barcodeMetricMap; + private final int maxNoCalls; + private final int maxMismatches; + private final int minMismatchDelta; + private final int minimumBaseQuality; + private final BarcodeMetric noMatchMetric; + + /** + * Construct a NewIlluminaDataProvider to create a ClusterData iterator over all clusters for a given tile. + * + * @param cbcls A list of cbcls to use when creating this data provider. + * @param filterFiles A list of the pf filter files to use when creating this data provider. + * @param barcodesMetrics A map of barcode to barcode metrics to output for this data provider. + * @param maxNoCalls The maximum number of no calls to allow in a match. + * @param maxMismatches The maximum number of mismatched calls to allow in a match. + * @param minMismatchDelta The minimum mismatch difference between the best and second best matches. + * @param minimumBaseQuality The minimum base quality to allow for a matching base call. + */ + NewIlluminaDataProvider(final List cbcls, final List locs, + final File[] filterFiles, final int lane, final int tileNum, final OutputMapping outputMapping, + boolean usingQualityScores, final Map barcodesMetrics, + final BarcodeMetric noMatchMetric, + int maxNoCalls, int maxMismatches, int minMismatchDelta, int minimumBaseQuality) { + super(lane, outputMapping); + this.usingQualityScores = usingQualityScores; + this.barcodeMetricMap = barcodesMetrics; + this.maxNoCalls = maxNoCalls; + this.maxMismatches = maxMismatches; + this.minMismatchDelta = minMismatchDelta; + this.minimumBaseQuality = minimumBaseQuality; + Map filterFileMap = new HashMap<>(); + for (File filterFile : filterFiles) { + filterFileMap.put(fileToTile(filterFile.getName()), filterFile); + } + this.reader = new CbclReader(cbcls, filterFileMap, outputMapping.getOutputReadLengths(), tileNum, locs, false); + this.outputReadStructure = outputMapping.getOutputReadStructure(); + + this.noMatchMetric = noMatchMetric; + } + + @Override + public void close() { + reader.close(); + } + + @Override + public void seekToTile(int seekAfterFirstRead) { + + } + + @Override + public boolean hasNext() { + return reader.hasNext(); + } + + @Override + public ClusterData next() { + CbclData cbclData = reader.next(); + + if (cbclData == null) return null; + + final ClusterData cluster = new ClusterData(outputReadTypes); + cluster.setLane(lane); + cluster.setTile(cbclData.getTile()); + + final int[] barcodeIndices = outputReadStructure.sampleBarcodes.getIndices(); + addReadData(cluster, numReads, cbclData); + + final byte[][] barcodeSubsequences = new byte[barcodeIndices.length][]; + final byte[][] qualityScores = usingQualityScores ? new byte[barcodeIndices.length][] : null; + for (int i = 0; i < barcodeIndices.length; i++) { + barcodeSubsequences[i] = cluster.getRead(barcodeIndices[i]).getBases(); + if (usingQualityScores) qualityScores[i] = cluster.getRead(barcodeIndices[i]).getQualities(); + } + + + final ExtractIlluminaBarcodes.PerTileBarcodeExtractor.BarcodeMatch match = findBestBarcodeAndUpdateMetrics(barcodeSubsequences, qualityScores, + true, barcodeMetricMap, noMatchMetric, maxNoCalls, maxMismatches, + minMismatchDelta, minimumBaseQuality); + + if (match.isMatched()) { + cluster.setMatchedBarcode(match.getBarcode()); + } + return cluster; + } + + public static Integer fileToTile(final String fileName) { + final Matcher matcher = Pattern.compile("^s_\\d+_(\\d{1,5}).+").matcher(fileName); + if (!matcher.matches()) { + return null; + } + return Integer.parseInt(matcher.group(1)); + } +} diff --git a/src/main/java/picard/illumina/parser/ParameterizedFileUtil.java b/src/main/java/picard/illumina/parser/ParameterizedFileUtil.java index 9e062d582..1aa9693e7 100644 --- a/src/main/java/picard/illumina/parser/ParameterizedFileUtil.java +++ b/src/main/java/picard/illumina/parser/ParameterizedFileUtil.java @@ -149,9 +149,9 @@ private String makeLaneRegex(final String fileNameEndPattern, final int lane) { } /** - * The period separator is expected in the file extension, since some do not start with it + * Escape the period character. */ - private String escapePeriods(final String preEscaped) { + public static String escapePeriods(final String preEscaped) { return preEscaped .replaceAll("\\.", "\\."); //In the first one the \\ is inside a regex in the second it's NOT } diff --git a/src/main/java/picard/illumina/parser/PerTileFileUtil.java b/src/main/java/picard/illumina/parser/PerTileFileUtil.java index fa12df310..c6138fc55 100644 --- a/src/main/java/picard/illumina/parser/PerTileFileUtil.java +++ b/src/main/java/picard/illumina/parser/PerTileFileUtil.java @@ -22,9 +22,9 @@ public PerTileFileUtil(final String extension, final File base, super(true, extension, base, faker, lane, skipEmptyFiles); this.fileMap = getTiledFiles(base, matchPattern); if (!fileMap.isEmpty()) { - this.tiles = Collections.unmodifiableList(new ArrayList(this.fileMap.keySet())); + this.tiles = new ArrayList<>(this.fileMap.keySet()); } else { - this.tiles = new ArrayList(); + this.tiles = Collections.emptyList(); } } diff --git a/src/main/java/picard/illumina/parser/PerTilePerCycleFileUtil.java b/src/main/java/picard/illumina/parser/PerTilePerCycleFileUtil.java index 63af850bd..93c502ed8 100644 --- a/src/main/java/picard/illumina/parser/PerTilePerCycleFileUtil.java +++ b/src/main/java/picard/illumina/parser/PerTilePerCycleFileUtil.java @@ -8,7 +8,6 @@ import java.io.File; import java.io.IOException; import java.util.ArrayList; -import java.util.Collections; import java.util.HashMap; import java.util.HashSet; import java.util.LinkedList; @@ -60,7 +59,7 @@ protected CycleIlluminaFileMap getPerTilePerCycleFiles() { cycledMap.put(getCycleFromDir(cycleDir), fileMap); } - this.tiles = Collections.unmodifiableList(new ArrayList(uniqueTiles)); + this.tiles = new ArrayList<>(uniqueTiles); return cycledMap; } @@ -255,7 +254,7 @@ private String getFileForCycle(final int currentCycle, final int tile) { return "C" + currentCycle + ".1" + File.separator + "s_" + lane + "_" + tile + extension; } - private static int getCycleFromDir(final File tempCycleDir) { + public static int getCycleFromDir(final File tempCycleDir) { final String fileName = tempCycleDir.getName(); final Matcher matcher = IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN.matcher(fileName); diff --git a/src/main/java/picard/illumina/parser/TileMetricsUtil.java b/src/main/java/picard/illumina/parser/TileMetricsUtil.java index 656c7be86..1c4f28a2b 100644 --- a/src/main/java/picard/illumina/parser/TileMetricsUtil.java +++ b/src/main/java/picard/illumina/parser/TileMetricsUtil.java @@ -26,21 +26,24 @@ import htsjdk.samtools.ValidationStringency; import htsjdk.samtools.util.CollectionUtil; +import htsjdk.samtools.util.IOUtil; import htsjdk.samtools.util.IterableAdapter; import htsjdk.samtools.util.Log; import picard.PicardException; -import picard.illumina.CollectIlluminaLaneMetrics; +import picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader; import picard.illumina.parser.readers.TileMetricsOutReader; import picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics; import java.io.File; import java.io.FileNotFoundException; import java.util.ArrayList; +import java.util.Arrays; import java.util.Collection; import java.util.Collections; import java.util.HashMap; import java.util.Iterator; import java.util.LinkedList; +import java.util.List; import java.util.Map; import java.util.Set; import java.util.stream.Collectors; @@ -51,33 +54,77 @@ * @author mccowan */ public class TileMetricsUtil { - /** The path to the directory containing the tile metrics file relative to the basecalling directory. */ + + private static final Log log = Log.getInstance(TileMetricsUtil.class); + /** + * The cycle directory that contain the tile metrics output. (Cycle 25 for NovaSeq) + */ + public static String CYCLE_CONTAINING_TILE_METRICS = "C25.1"; + /** + * The path to the directory containing the tile metrics file relative to the basecalling directory. + */ public static String INTEROP_SUBDIRECTORY_NAME = "InterOp"; - - /** The expected name of the tile metrics output file. */ + + /** + * The expected name of the tile metrics output file. + */ public static String TILE_METRICS_OUT_FILE_NAME = "TileMetricsOut.bin"; private final static Log LOG = Log.getInstance(TileMetricsUtil.class); - /** Returns the path to the TileMetrics file given the basecalling directory. */ - public static File renderTileMetricsFileFromBasecallingDirectory(final File illuminaRunDirectory) { - return new File(new File(illuminaRunDirectory, INTEROP_SUBDIRECTORY_NAME), TILE_METRICS_OUT_FILE_NAME); + /** + * Returns the path to the TileMetrics file given the basecalling directory. + */ + public static File renderTileMetricsFileFromBasecallingDirectory(final File illuminaRunDirectory, boolean isNovaSeq) { + if (isNovaSeq) { + return new File(new File(illuminaRunDirectory, INTEROP_SUBDIRECTORY_NAME + File.separator + CYCLE_CONTAINING_TILE_METRICS), TILE_METRICS_OUT_FILE_NAME); + } else { + return new File(new File(illuminaRunDirectory, INTEROP_SUBDIRECTORY_NAME), TILE_METRICS_OUT_FILE_NAME); + } } - + + public static Collection parseTileMetrics(final File tileMetricsOutFile, + final Map phasingMetricsFiles, + final ReadStructure readStructure, + final ValidationStringency validationStringency) + throws FileNotFoundException { + TileMetricsOutReader tileMetricsIterator = new TileMetricsOutReader(tileMetricsOutFile, TileMetricsOutReader.TileMetricsVersion.THREE); + final Collection tileMetrics = determineLastValueForLaneTileMetricsCode(tileMetricsIterator); + final Map> locationToMetricsMap = partitionTileMetricsByLocation(tileMetrics); + final Collection tiles = new LinkedList<>(); + for (final Map.Entry> entry : locationToMetricsMap.entrySet()) { + final Collection tileRecords = entry.getValue(); + + final IlluminaTileMetrics record = CollectionUtil.getSoleElement(tileRecords); + + //only create for cluster records + if (record.isClusterRecord()) { + // Snag the phasing data for each read in the read structure. For both types of phasing values, this is the median of all of the individual values seen + final Collection tilePhasingValues = getTilePhasingValues(record.getLaneTileCode(), + phasingMetricsFiles, readStructure, validationStringency); + + tiles.add(new Tile(record.getLaneNumber(), record.getTileNumber(), tileMetricsIterator.getDensity(), record.getMetricValue(), + tilePhasingValues.toArray(new TilePhasingValue[tilePhasingValues.size()]))); + } + } + + return Collections.unmodifiableCollection(tiles); + } + /** * Returns an unmodifiable collection of tile data read from the provided file. For each tile we will extract: - * - lane number - * - tile number - * - density - * - cluster ID - * - Phasing & Prephasing for first template read (if available) - * - Phasing & Prephasing for second template read (if available) + * - lane number + * - tile number + * - density + * - cluster ID + * - Phasing & Prephasing for first template read (if available) + * - Phasing & Prephasing for second template read (if available) */ public static Collection parseTileMetrics(final File tileMetricsOutFile, final ReadStructure readStructure, final ValidationStringency validationStringency) throws FileNotFoundException { // Get the tile metrics lines from TileMetricsOut, keeping only the last value for any Lane/Tile/Code combination final Collection tileMetrics = determineLastValueForLaneTileMetricsCode(new TileMetricsOutReader - (tileMetricsOutFile)); + (tileMetricsOutFile, TileMetricsOutReader.TileMetricsVersion.TWO)); // Collect the tiles by lane & tile, and then collect the metrics by lane final Map> locationToMetricsMap = partitionTileMetricsByLocation(tileMetrics); @@ -100,13 +147,86 @@ public static File renderTileMetricsFileFromBasecallingDirectory(final File illu final Collection tilePhasingValues = getTilePhasingValues(codeMetricsMap, readStructure, validationStringency); tiles.add(new Tile(densityRecord.getLaneNumber(), densityRecord.getTileNumber(), densityRecord.getMetricValue(), clusterRecord.getMetricValue(), - tilePhasingValues.toArray(new TilePhasingValue[tilePhasingValues.size()]))); + tilePhasingValues.toArray(new TilePhasingValue[tilePhasingValues.size()]))); } return Collections.unmodifiableCollection(tiles); } - /** Pulls out the phasing & prephasing value for the template reads and returns a collection of TilePhasingValues representing these */ + private static Collection getTilePhasingValues(TileMetricsOutReader.IlluminaLaneTileCode tileCode, + Map phasingMetricFiles, + final ReadStructure readStructure, + final ValidationStringency validationStringency) { + final Collection tilePhasingValues = new ArrayList<>(); + int totalCycleCount = 0; + + boolean isFirstRead = true; + + int readNum = 0; + for (int outputLength : readStructure.readLengths) { + ReadDescriptor descriptor = readStructure.descriptors.get(readNum++); + if (descriptor.type == ReadType.Template) { + final TileTemplateRead tileTemplateRead = isFirstRead ? TileTemplateRead.FIRST : TileTemplateRead.SECOND; + + List cycleNumWithData = new ArrayList<>(); + Map>> phasing = new HashMap<>(); + Map>> prePhasing = new HashMap<>(); + for (int cycle = 0; cycle < outputLength; cycle++) { + File phasingData = phasingMetricFiles.get(totalCycleCount + 1); + if (phasingData != null) { + cycleNumWithData.add((float) (cycle + 1)); + EmpiricalPhasingMetricsOutReader reader = new EmpiricalPhasingMetricsOutReader(phasingData); + + while (reader.hasNext()) { + EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics phasingMetrics = reader.next(); + + TileMetricsOutReader.IlluminaLaneTileCode laneTileCode = phasingMetrics.laneTileCode; + int tileNumber = laneTileCode.getTileNumber(); + if (laneTileCode.getLaneNumber() != tileCode.getLaneNumber() + || tileNumber != tileCode.getTileNumber()) { + continue; + } + + if (!phasing.containsKey(tileNumber)) { + phasing.put(tileNumber, new HashMap<>()); + prePhasing.put(tileNumber, new HashMap<>()); + } + int laneNumber = laneTileCode.getLaneNumber(); + if (!phasing.get(tileNumber).containsKey(laneNumber)) { + phasing.get(tileNumber).put(laneNumber, new ArrayList<>()); + prePhasing.get(tileNumber).put(laneNumber, new ArrayList<>()); + } + phasing.get(tileNumber).get(laneNumber).add(phasingMetrics.phasingWeight); + prePhasing.get(tileNumber).get(laneNumber).add(phasingMetrics.prephasingWeight); + } + } + + totalCycleCount++; + } + + phasing.forEach((tileNum, lanePhasingMetrics) -> { + Map> lanePrePhasingMetrics = prePhasing.get(tileNum); + lanePhasingMetrics.forEach((laneNum, phasingMetrics) -> { + List prephasingMetrics = lanePrePhasingMetrics.get(laneNum); + float[] phasingSlopeAndOffset = computeLinearFit(cycleNumWithData.toArray(new Float[0]), phasingMetrics.toArray(new Float[0]), phasingMetrics.size()); + float[] prePhasingSlopeAndOffset = computeLinearFit(cycleNumWithData.toArray(new Float[0]), prephasingMetrics.toArray(new Float[0]), phasingMetrics.size()); + TilePhasingValue value = new TilePhasingValue(tileTemplateRead, phasingSlopeAndOffset[0], prePhasingSlopeAndOffset[0]); + tilePhasingValues.add(value); + }); + }); + + isFirstRead = false; + } else { + totalCycleCount += outputLength; + } + } + + return tilePhasingValues; + } + + /** + * Pulls out the phasing & prephasing value for the template reads and returns a collection of TilePhasingValues representing these + */ private static Collection getTilePhasingValues(final Map> codeMetricsMap, final ReadStructure readStructure, final ValidationStringency validationStringency) { boolean isFirstRead = true; final Collection tilePhasingValues = new ArrayList<>(); @@ -138,7 +258,7 @@ public static File renderTileMetricsFileFromBasecallingDirectory(final File illu } else { throw new PicardException(message); } - phasingValue = 0; + phasingValue = 0; prePhasingValue = 0; } @@ -150,7 +270,9 @@ public static File renderTileMetricsFileFromBasecallingDirectory(final File illu return tilePhasingValues; } - /** According to Illumina, for every lane/tile/code combination they will only use the last value. Filter out the previous values */ + /** + * According to Illumina, for every lane/tile/code combination they will only use the last value. Filter out the previous values + */ private static Collection determineLastValueForLaneTileMetricsCode(final Iterator tileMetricsIterator) { final Map filteredTileMetrics = new HashMap<>(); @@ -175,4 +297,90 @@ private static String renderMetricLocationKey(final IlluminaTileMetrics metric) return tileMetrics.stream().collect(Collectors.groupingBy(TileMetricsUtil::renderMetricLocationKey)); } + public static Map renderPhasingMetricsFilesFromBasecallingDirectory(File illuminaRunDirectory) { + File[] cycleDirs = IOUtil.getFilesMatchingRegexp(new File(illuminaRunDirectory, INTEROP_SUBDIRECTORY_NAME), + IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN); + + Map phasingMetrics = new HashMap<>(); + Arrays.asList(cycleDirs) + .forEach(cycleDir -> { + File[] filesMatchingRegexp = IOUtil.getFilesMatchingRegexp( + cycleDir, "EmpiricalPhasingMetricsOut.bin"); + if (filesMatchingRegexp.length > 0) { + phasingMetrics.put(PerTilePerCycleFileUtil.getCycleFromDir(cycleDir), + filesMatchingRegexp[0]); + } + }); + return phasingMetrics; + } + + /*line fit for phasing weights + /** Compute the best fit line (slope + offset) given the points defined by (x_values[i], y_values[i]) + * + * @param x_values X-values of the list of points + * @param y_values Y-values of the list of points + * @param slope slope of the best fit line (calculated by this function) + * @param offset offset of the best fit line (calculated by this function) + * @param sample_count number of weights to use for fitting + * @return true if linear fit could be computed, false if not + + bool compute_linear_fit(const std::vector& x_values, const std::vector& y_values, float& slope, float& offset, size_t sample_count=0) + { + if(sample_count==0 || sample_count > x_values.size()) sample_count = x_values.size(); + if (x_values.size() <= 1 || x_values.size() != y_values.size()) + { + //TODO: throw error? + return false; + } + float sx = 0; // Sum(x) + float sy = 0; // Sum(y) + float sxx = 0; // Sum(x*x) + float sxy = 0; // Sum(x*y) + for (size_t i = 0; i < sample_count; i++) + { + sx += x_values[i]; + sy += y_values[i]; + sxy += x_values[i] * y_values[i]; + sxx += x_values[i] * x_values[i]; + } + const float denominator = sample_count * sxx - sx * sx; + if (denominator > std::numeric_limits::epsilon()) + { + slope = (sample_count * sxy - sx * sy) / denominator; + offset = (sy * sxx - sx * sxy) / denominator; + return true; + } + return false; + }*/ + + private static float[] computeLinearFit(Float[] xValues, Float[] yValues, int sampleCount) { + if (sampleCount == 0 || sampleCount > xValues.length) sampleCount = xValues.length; + if (xValues.length <= 1 || xValues.length != yValues.length) { + throw new PicardException("Can not compute linear fit."); + } + + float sumX = 0; + float sumY = 0; + float sumXX = 0; + float sumXY = 0; + + //returns + float slope = 0f; + float offset = 0f; + + for (int i = 0; i < sampleCount; i++) { + sumX += xValues[i]; + sumY += yValues[i]; + sumXY += xValues[i] * yValues[i]; + sumXX += xValues[i] * xValues[i]; + } + + float denominator = sampleCount * sumXX - sumX * sumX; + + if (denominator > Math.ulp(denominator)) { + slope = (sampleCount * sumXY - sumX * sumY) / denominator; + offset = (sumY * sumXX - sumX * sumXY) / denominator; + } + return new float[]{slope, offset}; + } } diff --git a/src/main/java/picard/illumina/parser/readers/AbstractIlluminaPositionFileReader.java b/src/main/java/picard/illumina/parser/readers/AbstractIlluminaPositionFileReader.java index 7068a36b2..9486793d3 100644 --- a/src/main/java/picard/illumina/parser/readers/AbstractIlluminaPositionFileReader.java +++ b/src/main/java/picard/illumina/parser/readers/AbstractIlluminaPositionFileReader.java @@ -32,14 +32,14 @@ import java.util.regex.Pattern; /** - * The position files of Illumina are nearly the same form: Pos files consist of text based tabbed - * x-y coordinate float pairs, locs files are binary x-y float pairs, clocs are compressed binary - * x-y float pairs. Each of these file types we read sequentially and are really concerned with - * iterating over the coordinates and returning them as as they would appear in a QSeq file. - * Therefore, this abstract base class provides the basic functionality for iterating over - * the values found in these files and converting them into qseq style coordinates. - * - * Currently these readers also return lane/tile but this will be unnecessary in future releases. + * The position files of Illumina are nearly the same form: Pos files consist of text based tabbed + * x-y coordinate float pairs, locs files are binary x-y float pairs, clocs are compressed binary + * x-y float pairs. Each of these file types we read sequentially and are really concerned with + * iterating over the coordinates and returning them as as they would appear in a QSeq file. + * Therefore, this abstract base class provides the basic functionality for iterating over + * the values found in these files and converting them into qseq style coordinates. + *

+ * Currently these readers also return lane/tile but this will be unnecessary in future releases. */ public abstract class AbstractIlluminaPositionFileReader implements CloseableIterator { @@ -50,28 +50,41 @@ * negative values and see what happens. */ public static final float MIN_POS = -10.0f; + public static final String S_LOCS_FILE = "s.locs"; public class PositionInfo { - /** The x-position as it occurs in the file being read */ + /** + * The x-position as it occurs in the file being read + */ public final float xPos; - /** The y-position as it occurs in the file being read*/ + /** + * The y-position as it occurs in the file being read + */ public final float yPos; - /** The lane, which is determined from the file name*/ + /** + * The lane, which is determined from the file name + */ public final int lane; - /** The tile, which is determined from the file name*/ + /** + * The tile, which is determined from the file name + */ public final int tile; - /** The QSeq style x-coordinat, an integer = Math.round(xPos*10 + 1000)*/ + /** + * The QSeq style x-coordinat, an integer = Math.round(xPos*10 + 1000) + */ public final int xQseqCoord; - /** The QSeq style y-coordinates, an integer = Math.round(yPos*10 + 1000)*/ + /** + * The QSeq style y-coordinates, an integer = Math.round(yPos*10 + 1000) + */ public final int yQseqCoord; public PositionInfo(final float x, final float y, final int lane, final int tile) { - if(x < MIN_POS || y < MIN_POS || x > MAX_POS || y > MAX_POS) { + if (x < MIN_POS || y < MIN_POS || x > MAX_POS || y > MAX_POS) { throw new IllegalArgumentException( String.format("Cluster location not in the range %f..%f. x: %f; y: %f; lane: %d; tile: %d", @@ -86,20 +99,22 @@ public PositionInfo(final float x, final float y, final int lane, final int tile this.tile = tile; } - /** Convert a value in float form as it occurs in pos,locs,and clocs files into integer as it is found in QSeqs */ + /** + * Convert a value in float form as it occurs in pos,locs,and clocs files into integer as it is found in QSeqs + */ private int posToQSeqCoord(final float pos) { return Math.round(pos * 10 + 1000); } public boolean equals(final Object other) { - if(other == null || other.getClass() != AbstractIlluminaPositionFileReader.PositionInfo.class) { + if (other == null || other.getClass() != AbstractIlluminaPositionFileReader.PositionInfo.class) { return false; } - if(other == this) return true; + if (other == this) return true; final PositionInfo otherPi = (PositionInfo) other; - return this.xPos == otherPi.xPos && this.yPos == otherPi.yPos && - this.lane == otherPi.lane && this.tile == otherPi.tile && - this.xQseqCoord == otherPi.xQseqCoord && this.yQseqCoord == otherPi.yQseqCoord; + return this.xPos == otherPi.xPos && this.yPos == otherPi.yPos && + this.lane == otherPi.lane && this.tile == otherPi.tile && + this.xQseqCoord == otherPi.xQseqCoord && this.yQseqCoord == otherPi.yQseqCoord; } } @@ -113,16 +128,22 @@ public boolean equals(final Object other) { public AbstractIlluminaPositionFileReader(final File file) { this.file = file; - final int [] laneAndTile = fileNameToLaneAndTile(file.getName()); - lane = laneAndTile[0]; - tile = laneAndTile[1]; + if (file.getName().equals(S_LOCS_FILE)) { + lane = 0; + tile = 0; + } else { + final int[] laneAndTile = fileNameToLaneAndTile(file.getName()); + lane = laneAndTile[0]; + tile = laneAndTile[1]; + } } /** * Use this ctor if lane and tile are not discernible from file name. - * @param file - * @param lane - * @param tile + * + * @param file The position file to read. + * @param lane The lane to read positions for. + * @param tile The tile to read positions for. */ public AbstractIlluminaPositionFileReader(final File file, final int lane, final int tile) { this.file = file; @@ -142,33 +163,43 @@ public File getFile() { return file; } - /** Extract the lane/tile from the given filename **/ - private int [] fileNameToLaneAndTile(final String fileName) { - final String [] tokens = fileName.split(File.pathSeparator); + /** + * Extract the lane/tile from the given filename + **/ + private int[] fileNameToLaneAndTile(final String fileName) { + final String[] tokens = fileName.split(File.pathSeparator); final Matcher matcher = FileNamePattern.matcher(tokens[tokens.length - 1]); - if(!matcher.matches()) { + if (!matcher.matches()) { throw new PicardException("File name not of the right structure: /s__(_pos.txt|_pos.txt.gz|_pos.txt.bz2.locs|.clocs). File name (" + fileName + ")"); } return new int[]{Integer.parseInt(matcher.group(1)), Integer.parseInt(matcher.group(2))}; } - /** Return the next set of coordinates in a given file. **/ + /** + * Return the next set of coordinates in a given file. + **/ public final PositionInfo next() { - if(! hasNext()) { - throw new NoSuchElementException("No such cluster, cluster count(" + makeExceptionMsg() +")"); + if (!hasNext()) { + throw new NoSuchElementException("No such cluster, cluster count(" + makeExceptionMsg() + ")"); } return unsafeNextInfo(); } - /** Returns the next position info. Implementations of this method do not need to call hasNext since - * it is called in next() */ + /** + * Returns the next position info. Implementations of this method do not need to call hasNext since + * it is called in next() + */ protected abstract PositionInfo unsafeNextInfo(); - /** Create a string that will be included in any NoSuchElementException thrown by the next() method */ + /** + * Create a string that will be included in any NoSuchElementException thrown by the next() method + */ protected abstract String makeExceptionMsg(); - /** Return true if the file has more elements to return, false otherwise */ + /** + * Return true if the file has more elements to return, false otherwise + */ public abstract boolean hasNext(); public void remove() { diff --git a/src/main/java/picard/illumina/parser/readers/BaseBclReader.java b/src/main/java/picard/illumina/parser/readers/BaseBclReader.java index 30783722a..74c214aae 100644 --- a/src/main/java/picard/illumina/parser/readers/BaseBclReader.java +++ b/src/main/java/picard/illumina/parser/readers/BaseBclReader.java @@ -13,7 +13,7 @@ import java.io.InputStream; import java.util.zip.GZIPInputStream; -class BaseBclReader { +public class BaseBclReader { private static final byte BASE_MASK = 0x0003; private static final byte[] BASE_LOOKUP = new byte[]{'A', 'C', 'G', 'T'}; final InputStream[] streams; @@ -52,15 +52,11 @@ this.numClustersPerCycle = new int[cycles]; } - int getNumCycles() { - return cycles; - } - int getNumClusters() { return numClustersPerCycle[0]; } - InputStream open(final File file, final boolean seekable, final boolean isGzip, final boolean isBgzf) throws IOException { + InputStream open(final File file, final boolean seekable, final boolean isGzip, final boolean isBgzf) { final String filePath = file.getAbsolutePath(); try { @@ -112,7 +108,7 @@ void decodeQualityBinnedBasecall(final BclData bclData, final int read, final in } } - class CycleData { + public class CycleData { final short version; final int headerSize; @@ -120,14 +116,13 @@ void decodeQualityBinnedBasecall(final BclData bclData, final int read, final in final byte bitsPerQualityScore; final int numberOfBins; final byte[] qualityBins; - final int numTiles; - final TileData[] tileInfo; + final TileData tileInfo; final boolean pfExcluded; CycleData(final short version, final int headerSize, final byte bitsPerBasecall, final byte bitsPerQualityScore, final int numberOfBins, final byte[] qualityBins, - final int numTiles, final TileData[] tileInfo, final boolean pfExcluded) { + final int numTiles, final TileData tileInfo, final boolean pfExcluded) { this.version = version; this.headerSize = headerSize; this.bitsPerBasecall = bitsPerBasecall; @@ -139,22 +134,34 @@ void decodeQualityBinnedBasecall(final BclData bclData, final int read, final in this.pfExcluded = pfExcluded; } - + public TileData getTileInfo() { + return tileInfo; + } } - class TileData { + public class TileData { final int tileNum; final int numClustersInTile; final int uncompressedBlockSize; final int compressedBlockSize; + final long filePosition; TileData(final int tileNum, final int numClustersInTile, final int uncompressedBlockSize, - final int compressedBlockSize) { + final int compressedBlockSize, long filePosition) { this.tileNum = tileNum; this.numClustersInTile = numClustersInTile; this.uncompressedBlockSize = uncompressedBlockSize; this.compressedBlockSize = compressedBlockSize; + this.filePosition = filePosition; + } + + public int getCompressedBlockSize() { + return compressedBlockSize; + } + + public int getNumClustersInTile() { + return numClustersInTile; } } } diff --git a/src/main/java/picard/illumina/parser/readers/CbclReader.java b/src/main/java/picard/illumina/parser/readers/CbclReader.java index 8557a394a..e8f1b94c9 100644 --- a/src/main/java/picard/illumina/parser/readers/CbclReader.java +++ b/src/main/java/picard/illumina/parser/readers/CbclReader.java @@ -3,20 +3,26 @@ import htsjdk.samtools.util.CloseableIterator; import htsjdk.samtools.util.CloserUtil; import htsjdk.samtools.util.Log; -import htsjdk.samtools.util.ProgressLogger; import htsjdk.samtools.util.RuntimeIOException; -import picard.illumina.parser.BclData; +import picard.PicardException; +import picard.illumina.parser.CbclData; import java.io.ByteArrayInputStream; +import java.io.EOFException; import java.io.File; import java.io.IOException; import java.io.InputStream; import java.nio.ByteBuffer; import java.nio.ByteOrder; import java.util.ArrayList; +import java.util.Arrays; import java.util.HashMap; +import java.util.Iterator; import java.util.List; import java.util.Map; +import java.util.TreeMap; +import java.util.regex.Matcher; +import java.util.regex.Pattern; import java.util.zip.GZIPInputStream; /** @@ -28,7 +34,7 @@ *

* q-val mapping info * Bytes 0-3 Number of bins (B), zero indicates no mapping - * B pairs of 4 byte values (if B > 0) {from, to}, {from, to}, {from, to} …from: quality score bin to: quality score + * B pairs of 4 byte values (if B > 0) {from, to}, {from, to}, {from, to} from: quality score bin to: quality score *

* Number of tile records unsigned 32bits little endian integer *

@@ -37,7 +43,7 @@ * Bytes 4-7 Number of clusters that were written into the current block (required due to bit-packed q-scores) * unsigned 32 bit integer *

- * Bytes 8-11 Uncompressed block size of the tile data (useful for sanity check whenexcluding non-PF clusters) + * Bytes 8-11 Uncompressed block size of the tile data (useful for sanity check when excluding non-PF clusters) * unsigned 32 bit integer *

* Bytes 12-15 Compressed block size of the tile data unsigned 32 bit integer @@ -57,117 +63,194 @@ * higher 4 bits are the second cluster. **/ -public class CbclReader extends BaseBclReader implements CloseableIterator { +public class CbclReader extends BaseBclReader implements CloseableIterator { - private static Log log = Log.getInstance(CbclReader.class); - - private ByteBuffer[] cachedTile; - - private int[] currentTile; - - private List queue = new ArrayList<>(); + private final byte[][] cachedTile; + private final int[] cachedTilePosition; + private CbclData queue = null; + private Iterator positionInfoIterator; private final CycleData[] cycleData; - private Map filters; - private Map cachedFilter = new HashMap<>(); - - void addFilters(Map filters) { - this.filters = filters; - } + private final Map filterFileMap; + private final Map cachedFilter = new HashMap<>(); + private final Map> surfaceToTileToCbclMap; + private int headerSize; + private Map> allTiles = new HashMap<>(); private static final int INITIAL_HEADER_SIZE = 6; + private static final Log log = Log.getInstance(CbclReader.class); + public static final Pattern PATTERN = Pattern.compile("^.+C(\\d{1,4}).+L(\\d{1,3})_(\\d).cbcl$"); - public CbclReader(final List cbcls, final int[] outputLengths) { + public CbclReader(final List cbcls, final Map filterFileMap, final int[] outputLengths, + int tileNum, List locs, boolean headerOnly) { super(outputLengths); + surfaceToTileToCbclMap = sortCbcls(cbcls); + this.filterFileMap = filterFileMap; cycleData = new CycleData[cycles]; - cachedTile = new ByteBuffer[cycles]; - currentTile = new int[cycles]; + cachedTile = new byte[cycles][]; + cachedTilePosition = new int[cycles]; + for (int i = 1; i <= cycles; i++) { + allTiles.put(i, new ArrayList<>()); + } + try { + readSurfaceTile(tileNum, locs, headerOnly); + } finally { + close(); + } + } + private void readSurfaceTile(int tileNum, List locs, + boolean headerOnly) { + log.info("Processing tile " + tileNum); try { - final ByteBuffer byteBuffer = ByteBuffer.allocate(INITIAL_HEADER_SIZE); - byteBuffer.order(ByteOrder.LITTLE_ENDIAN); - for (int i = 0; i < cycles; i++) { - currentTile[i] = 0; - final File bclFile = cbcls.get(i); - - final InputStream stream = open(bclFile, false, false, false); - int read = stream.read(byteBuffer.array()); - - //we need to read the first 6 bytes to determine the header size - if (read != INITIAL_HEADER_SIZE) { - close(); - throw new RuntimeIOException(String.format("BCL %s has invalid header structure.", bclFile.getAbsoluteFile())); - } + for (Map.Entry> entry : surfaceToTileToCbclMap.entrySet()) { + Map cycleMap = entry.getValue(); + for (int i = 0; i < cycles; i++) { + //cycleMap is 1 indexed + final ByteBuffer byteBuffer = ByteBuffer.allocate(INITIAL_HEADER_SIZE); + byteBuffer.order(ByteOrder.LITTLE_ENDIAN); + + final File bclFile = cycleMap.get(i + 1); + if (bclFile == null) { + throw new PicardException("Expected cbcl file for surface " + entry.getKey() + " cycle " + (i + 1) + " but it was not found."); + } - short version = byteBuffer.getShort(); - int headerSize = byteBuffer.getInt(); + final InputStream stream = open(bclFile, false, false, false); + int read = stream.read(byteBuffer.array()); - final ByteBuffer headerBuffer = ByteBuffer.allocate(headerSize - INITIAL_HEADER_SIZE); - headerBuffer.order(ByteOrder.LITTLE_ENDIAN); + //we need to read the first 6 bytes to determine the header size + if (read != INITIAL_HEADER_SIZE) { + throw new RuntimeIOException(String.format("BCL %s has invalid header structure.", bclFile.getAbsoluteFile())); + } - read = stream.read(headerBuffer.array()); - if (read != headerSize - INITIAL_HEADER_SIZE) { - close(); - throw new RuntimeIOException(String.format("BCL %s has invalid header structure.", bclFile.getAbsoluteFile())); - } + short version = byteBuffer.getShort(); + headerSize = byteBuffer.getInt(); - byte bitsPerBasecall = headerBuffer.get(); - byte bitsPerQualityScore = headerBuffer.get(); + final ByteBuffer headerBuffer = ByteBuffer.allocate(headerSize - INITIAL_HEADER_SIZE); + headerBuffer.order(ByteOrder.LITTLE_ENDIAN); - if (bitsPerBasecall != 2 && bitsPerBasecall != bitsPerQualityScore) { - close(); - throw new RuntimeIOException("CBCL data not encoded in nibbles. (not currently supported)"); - } + read = stream.read(headerBuffer.array()); + if (read != headerSize - INITIAL_HEADER_SIZE) { + throw new PicardException(String.format("BCL %s has invalid header structure.", bclFile.getAbsoluteFile())); + } - int numberOfBins = headerBuffer.getInt(); + byte bitsPerBasecall = headerBuffer.get(); + byte bitsPerQualityScore = headerBuffer.get(); - byte[] qualityBins = new byte[numberOfBins]; - //each bin has a pair of 4 byte mappings - for (int j = 0; j < numberOfBins; j++) { - headerBuffer.getInt(); // first int is "from" value, which we don't need - int to = headerBuffer.getInt(); - qualityBins[j] = (byte) to; - } + if (bitsPerBasecall != 2 && bitsPerBasecall != bitsPerQualityScore) { + throw new PicardException("CBCL data not encoded in nibbles. (not currently supported) bitsPerBasecall : " + + bitsPerBasecall + " bitsPerQualityScore : " + bitsPerQualityScore); + } + + int numberOfBins = headerBuffer.getInt(); + + byte[] qualityBins = new byte[numberOfBins]; + //each bin has a pair of 4 byte mappings + for (int j = 0; j < numberOfBins; j++) { + headerBuffer.getInt(); // first int is "from" value, which we don't need + int to = headerBuffer.getInt(); + qualityBins[j] = (byte) to; + } + long filePos = 0; + + int numTiles = headerBuffer.getInt(); + TileData tileInfo = null; + for (int j = 0; j < numTiles; j++) { + int tile = headerBuffer.getInt(); + int numClustersInTile = headerBuffer.getInt(); + int uncompressedBlockSize = headerBuffer.getInt(); + int compressedBlockSize = headerBuffer.getInt(); + TileData tileData = new TileData(tile, numClustersInTile, uncompressedBlockSize, compressedBlockSize, filePos); + allTiles.get(i + 1).add(tileData); + if (tile == tileNum) { + tileInfo = tileData; + } + filePos += compressedBlockSize; + } + + boolean pfExcluded = headerBuffer.get() == 1; + //try the next surface if we didn't find the tile + if (tileInfo == null) { + continue; + } - int numTiles = headerBuffer.getInt(); - TileData[] tileInfo = new TileData[numTiles]; - for (int j = 0; j < numTiles; j++) { - int tileNum = headerBuffer.getInt(); - int numClustersInTile = headerBuffer.getInt(); - int uncompressedBlockSize = headerBuffer.getInt(); - int compressedBlockSize = headerBuffer.getInt(); - tileInfo[j] = new TileData(tileNum, numClustersInTile, uncompressedBlockSize, compressedBlockSize); + cycleData[i] = new CycleData(version, headerSize, bitsPerBasecall, bitsPerQualityScore, numberOfBins, qualityBins, numTiles, tileInfo, pfExcluded); + this.streams[i] = stream; + this.streamFiles[i] = bclFile; + byteBuffer.clear(); + headerBuffer.clear(); } + } - boolean pfExcluded = headerBuffer.get() == 1; - cycleData[i] = new CycleData(version, headerSize, bitsPerBasecall, bitsPerQualityScore, numberOfBins, qualityBins, numTiles, tileInfo, pfExcluded); - this.streams[i] = stream; - this.streamFiles[i] = bclFile; - byteBuffer.clear(); - headerBuffer.clear(); + if (headerOnly) { + return; } + int totalCycleCount = 0; + + if (cycleData[totalCycleCount].tileInfo == null) { + throw new PicardException("Could not find tile " + tileNum); + } + + for (int outputLength : outputLengths) { + for (int cycle = 0; cycle < outputLength; cycle++) { + CycleData currentCycleData = cycleData[totalCycleCount]; + try { + if (cachedTile[totalCycleCount] == null) { + if (!cachedFilter.containsKey(cycleData[totalCycleCount].tileInfo.tileNum)) { + cacheFilterAndLocs(cycleData[totalCycleCount].tileInfo, locs); + } + cacheTile(totalCycleCount, cycleData[totalCycleCount].tileInfo, currentCycleData); + } + } catch (IOException e) { + // when logging the error, increment cycle by 1, since totalCycleCount is zero-indexed but Illumina directories are 1-indexed. + throw new PicardException(String.format("Error while reading from BCL file for cycle %d. Offending file on disk is %s", + (totalCycleCount + 1), this.streamFiles[totalCycleCount].getAbsolutePath()), e); + } + totalCycleCount++; + } + } } catch (final IOException ioe) { throw new RuntimeIOException(ioe); } } + private Map> sortCbcls(List cbcls) { + Map> sortedMap = new TreeMap<>(); + for (File cbcl : cbcls) { + Matcher matcher = PATTERN.matcher(cbcl.getAbsolutePath()); + if (!matcher.matches()) { + throw new PicardException("CBCL File " + cbcl.getAbsolutePath() + " does not match expected pattern."); + } + Integer surface = Integer.valueOf(matcher.group(3)); + Integer cycle = Integer.valueOf(matcher.group(1)); + if (sortedMap.containsKey(surface)) { + sortedMap.get(surface).put(cycle, cbcl); + } else { + Map cycleMap = new HashMap<>(); + cycleMap.put(cycle, cbcl); + sortedMap.put(surface, cycleMap); + } + } + + return sortedMap; + } + @Override public boolean hasNext() { - if (queue.isEmpty()) { + if (queue == null) { advance(); } - return !queue.isEmpty(); + return queue != null; } - public BclData next() { - if (queue.isEmpty()) { + public CbclData next() { + if (queue == null) { advance(); } - - final BclData data = queue.get(0); - queue.remove(0); + CbclData data = queue; + queue = null; return data; } @@ -180,126 +263,147 @@ public void close() { private void advance() { int totalCycleCount = 0; - BclData data = new BclData(outputLengths); + CbclData data = new CbclData(outputLengths, cycleData[totalCycleCount].tileInfo.tileNum); for (int read = 0; read < outputLengths.length; read++) { for (int cycle = 0; cycle < outputLengths[read]; cycle++) { - try { - CycleData currentCycleData = cycleData[totalCycleCount]; - TileData currentTileData = currentCycleData.tileInfo[currentTile[totalCycleCount]]; - try { - if (cachedTile[totalCycleCount] == null) { - if (!cachedFilter.containsKey(currentTileData.tileNum)) { - cacheFilter(currentTileData); - } - cacheTile(totalCycleCount, currentTileData, currentCycleData); - } - } catch (IOException e) { - // when logging the error, increment cycle by 1, since totalCycleCount is zero-indexed but Illumina directories are 1-indexed. - throw new IOException(String.format("Error while reading from BCL file for cycle %d. Offending file on disk is %s", - (totalCycleCount + 1), this.streamFiles[totalCycleCount].getAbsolutePath()), e); - } - - if (!cachedTile[totalCycleCount].hasRemaining()) { - //on to the next tile - currentTile[totalCycleCount]++; - //if past the last tile then return - if (currentTile[totalCycleCount] > currentCycleData.tileInfo.length - 1) { - return; - } - currentTileData = currentCycleData.tileInfo[currentTile[totalCycleCount]]; - if (!cachedFilter.containsKey(currentTileData.tileNum)) { - cacheFilter(currentTileData); - } - cacheTile(totalCycleCount, currentTileData, currentCycleData); - } + CycleData currentCycleData = cycleData[totalCycleCount]; - int singleByte = cachedTile[totalCycleCount].get(); + if (cachedTilePosition[totalCycleCount] >= cachedTile[totalCycleCount].length) { + // end of tile + return; + } - decodeQualityBinnedBasecall(data, read, cycle, singleByte, currentCycleData); + int singleByte = cachedTile[totalCycleCount][cachedTilePosition[totalCycleCount]++]; - totalCycleCount++; - } catch (final IOException ioe) { - throw new RuntimeIOException(ioe); - } + decodeQualityBinnedBasecall(data, read, cycle, singleByte, currentCycleData); + totalCycleCount++; } } - this.queue.add(data); + data.setPositionInfo(positionInfoIterator.next()); + this.queue = data; } - private void cacheFilter(TileData currentTileData) { + private void cacheFilterAndLocs(TileData currentTileData, List locs) { boolean[] filterValues = new boolean[currentTileData.numClustersInTile]; - FilterFileReader reader = new FilterFileReader(filters.get(currentTileData.tileNum)); + FilterFileReader reader = new FilterFileReader(filterFileMap.get(currentTileData.tileNum)); + Iterator positionInfoIterator = locs.iterator(); int count = 0; while (reader.hasNext()) { filterValues[count] = reader.next(); count++; } + + List positions = new ArrayList<>(); + for (boolean filterValue : filterValues) { + AbstractIlluminaPositionFileReader.PositionInfo info = positionInfoIterator.next(); + if (filterValue) { + positions.add(info); + } + } + this.positionInfoIterator = positions.iterator(); cachedFilter.put(currentTileData.tileNum, filterValues); } private void cacheTile(int totalCycleCount, TileData tileData, CycleData currentCycleData) throws IOException { - ByteBuffer tileByteBuffer = ByteBuffer.allocate(tileData.compressedBlockSize); + byte[] tileByteArray = new byte[tileData.compressedBlockSize]; //we are going to explode the nibbles in to bytes to make PF filtering easier - ByteBuffer tempUncompressedByteBuffer = ByteBuffer.allocate(tileData.uncompressedBlockSize); - ByteBuffer uncompressedByteBuffer = ByteBuffer.allocate(tileData.uncompressedBlockSize); - ByteBuffer unNibbledByteBuffer = ByteBuffer.allocate(tileData.uncompressedBlockSize * 2); - - tileByteBuffer.order(ByteOrder.LITTLE_ENDIAN); - uncompressedByteBuffer.order(ByteOrder.LITTLE_ENDIAN); + byte[] uncompressedByteArray = new byte[tileData.uncompressedBlockSize]; + // ByteBuffer uncompressedByteArray = ByteBuffer.allocate(tileData.uncompressedBlockSize); + byte[] unNibbledByteArray = new byte[tileData.uncompressedBlockSize * 2]; // Read the whole compressed block into a buffer, then sanity check the length - int readBytes = this.streams[totalCycleCount].read(tileByteBuffer.array()); + InputStream stream = this.streams[totalCycleCount]; + long dataLeft = tileData.filePosition - stream.skip(tileData.filePosition); + while (dataLeft > 0) { + dataLeft -= stream.skip(dataLeft); + } + + int readBytes = stream.read(tileByteArray); if (readBytes != tileData.compressedBlockSize) { - throw new IOException(String.format("Error while reading from BCL file for cycle %d. Offending file on disk is %s", + throw new PicardException(String.format("Error while reading from BCL file for cycle %d. Offending file on disk is %s", (totalCycleCount + 1), this.streamFiles[totalCycleCount].getAbsolutePath())); } // Uncompress the data from the buffer we just wrote - use gzip input stream to write to uncompressed buffer - ByteArrayInputStream byteInputStream = new ByteArrayInputStream(tileByteBuffer.array()); - if (cachedTile[totalCycleCount] != null) { - //clear the old cache - cachedTile[totalCycleCount] = null; - } - GZIPInputStream gzipInputStream = new GZIPInputStream(byteInputStream, uncompressedByteBuffer.capacity()); - int read = 0; + ByteArrayInputStream byteInputStream = new ByteArrayInputStream(Arrays.copyOfRange(tileByteArray, 0, readBytes)); + + GZIPInputStream gzipInputStream = new GZIPInputStream(byteInputStream, uncompressedByteArray.length); + int read; int totalRead = 0; - while ((read = gzipInputStream.read(tempUncompressedByteBuffer.array(), 0, tempUncompressedByteBuffer.capacity())) != -1) { - uncompressedByteBuffer.put(tempUncompressedByteBuffer.array(), 0, read); - totalRead += read; + try { + while ((read = gzipInputStream.read(uncompressedByteArray, totalRead, uncompressedByteArray.length - totalRead)) != -1) { + if (read == 0) break; + totalRead += read; + } + } catch (EOFException eofException) { + throw new PicardException("Unexpected end of file " + this.streamFiles[totalCycleCount].getAbsolutePath() + + " this file is likely corrupt or truncated. We have read " + + totalRead + " and were expecting to read " + + uncompressedByteArray.length); } if (totalRead != tileData.uncompressedBlockSize) { - throw new IOException(String.format("Error while decompressing from BCL file for cycle %d. Offending file on disk is %s", + throw new PicardException(String.format("Error while decompressing from BCL file for cycle %d. Offending file on disk is %s", (totalCycleCount + 1), this.streamFiles[totalCycleCount].getAbsolutePath())); } // Read uncompressed data from the buffer and expand each nibble into a full byte for ease of use - uncompressedByteBuffer.flip(); - while (uncompressedByteBuffer.hasRemaining()) { - byte singleByte = uncompressedByteBuffer.get(); - unNibbledByteBuffer.put((byte) (singleByte & 0x0f)); - unNibbledByteBuffer.put((byte) ((singleByte >> 4) & 0x0f)); + int index = 0; + for (byte singleByte : uncompressedByteArray) { + unNibbledByteArray[index] = (byte) (singleByte & 0x0f); + index++; + unNibbledByteArray[index] = (byte) ((singleByte >> 4) & 0x0f); + index++; } gzipInputStream.close(); // Write buffer contents to cached tile array - unNibbledByteBuffer.flip(); - //if nonPF reads are included we need to strip them out + // if nonPF reads are included we need to strip them out if (!currentCycleData.pfExcluded) { - ByteBuffer uncompressedFilteredByteBuffer = ByteBuffer.allocate(tileData.uncompressedBlockSize * 2); - FilterFileReader reader = new FilterFileReader(filters.get(tileData.tileNum)); - while (reader.hasNext()) { - byte readByte = unNibbledByteBuffer.get(); - if (reader.next()) { - uncompressedFilteredByteBuffer.put(readByte); + boolean[] filterDatas = cachedFilter.get(tileData.tileNum); + int sum = 0; + for (boolean b : filterDatas) { + sum += b ? 1 : 0; + } + byte[] filteredByteArray = new byte[sum]; + int filterIndex = 0; + int basecallIndex = 0; + for (boolean filterData : filterDatas) { + byte readByte = unNibbledByteArray[filterIndex]; + if (filterData) { + filteredByteArray[basecallIndex] = readByte; + basecallIndex++; } + filterIndex++; } - uncompressedFilteredByteBuffer.flip(); - cachedTile[totalCycleCount] = uncompressedFilteredByteBuffer.slice(); + cachedTile[totalCycleCount] = filteredByteArray; } else { - cachedTile[totalCycleCount] = unNibbledByteBuffer; + cachedTile[totalCycleCount] = unNibbledByteArray; } + cachedTilePosition[totalCycleCount] = 0; + } + + public CycleData[] getCycleData() { + return cycleData; + } + + public int getHeaderSize() { + return headerSize; + } + + public List getFilesForCycle(int i) { + List cbclFiles = new ArrayList<>(); + surfaceToTileToCbclMap.values().forEach(map -> { + if (map.containsKey(i)) { + cbclFiles.add(map.get(i)); + } + }); + return cbclFiles; + } + + public Map> getAllTiles() { + return allTiles; } } diff --git a/src/main/java/picard/illumina/parser/readers/EmpiricalPhasingMetricsOutReader.java b/src/main/java/picard/illumina/parser/readers/EmpiricalPhasingMetricsOutReader.java new file mode 100644 index 000000000..d9d94be74 --- /dev/null +++ b/src/main/java/picard/illumina/parser/readers/EmpiricalPhasingMetricsOutReader.java @@ -0,0 +1,47 @@ +package picard.illumina.parser.readers; + +import picard.util.UnsignedTypeUtil; + +import java.io.File; +import java.nio.ByteBuffer; +import java.util.Iterator; +import java.util.NoSuchElementException; + +public class EmpiricalPhasingMetricsOutReader implements Iterator { + private static final int HEADER_SIZE = 2; + private static final int RECORD_SIZE = 16; + + private final BinaryFileIterator bbIterator; + + public EmpiricalPhasingMetricsOutReader(File phasingMetricsOutFile) { + bbIterator = MMapBackedIteratorFactory.getByteBufferIterator(HEADER_SIZE, RECORD_SIZE, phasingMetricsOutFile); + bbIterator.getHeaderBytes(); + } + + @Override + public boolean hasNext() { + return bbIterator.hasNext(); + } + + @Override + public IlluminaPhasingMetrics next() { + if (!hasNext()) { + throw new NoSuchElementException(); + } + return new IlluminaPhasingMetrics(bbIterator.next()); + } + + public static class IlluminaPhasingMetrics { + public final TileMetricsOutReader.IlluminaLaneTileCode laneTileCode; + public final int cycle; + public final float phasingWeight; + public final float prephasingWeight; + + IlluminaPhasingMetrics(final ByteBuffer bb) { + this.laneTileCode = new TileMetricsOutReader.IlluminaLaneTileCode(UnsignedTypeUtil.uShortToInt(bb.getShort()), bb.getInt(), 0); + this.cycle = UnsignedTypeUtil.uShortToInt(bb.getShort()); + this.phasingWeight = bb.getFloat(); + this.prephasingWeight = bb.getFloat(); + } + } +} diff --git a/src/main/java/picard/illumina/parser/readers/TileMetricsOutReader.java b/src/main/java/picard/illumina/parser/readers/TileMetricsOutReader.java index 215e067c2..9b3d8657e 100644 --- a/src/main/java/picard/illumina/parser/readers/TileMetricsOutReader.java +++ b/src/main/java/picard/illumina/parser/readers/TileMetricsOutReader.java @@ -27,30 +27,33 @@ * byte 6-9 (float) = metrics value, see Theory of RTA document by Illumina for definition */ public class TileMetricsOutReader implements Iterator { - private static final int HEADER_SIZE = 2; - private static final int EXPECTED_RECORD_SIZE = 10; - private static final int EXPECTED_VERSION = 2; - private final BinaryFileIterator bbIterator; + private float density; + private TileMetricsVersion version; /** * Return a TileMetricsOutReader for the specified file * @param tileMetricsOutFile The file to read + * @param version The version of the tile metrics file being parsed. */ - public TileMetricsOutReader(final File tileMetricsOutFile) { - bbIterator = MMapBackedIteratorFactory.getByteBufferIterator(HEADER_SIZE, EXPECTED_RECORD_SIZE, tileMetricsOutFile); + public TileMetricsOutReader(final File tileMetricsOutFile, TileMetricsOutReader.TileMetricsVersion version) { + + bbIterator = MMapBackedIteratorFactory.getByteBufferIterator(version.headerSize, version.recordSize, tileMetricsOutFile); + this.version = version; final ByteBuffer header = bbIterator.getHeaderBytes(); - //Get the version, should be EXPECTED_VERSION, which is 2 final int actualVersion = UnsignedTypeUtil.uByteToInt(header.get()); - if(actualVersion != EXPECTED_VERSION) { - throw new PicardException("TileMetricsOutReader expects the version number to be " + EXPECTED_VERSION + ". Actual Version in Header( " + actualVersion + ")" ); + if (actualVersion != version.version) { + throw new PicardException("TileMetricsOutReader expects the version number to be " + version.version + ". Actual Version in Header( " + actualVersion + ")"); } final int actualRecordSize = UnsignedTypeUtil.uByteToInt(header.get()); - if(EXPECTED_RECORD_SIZE != actualRecordSize) { - throw new PicardException("TileMetricsOutReader expects the record size to be " + EXPECTED_RECORD_SIZE + ". Actual Record Size in Header( " + actualRecordSize + ")" ); + if (version.recordSize != actualRecordSize) { + throw new PicardException("TileMetricsOutReader expects the record size to be " + version.recordSize + ". Actual Record Size in Header( " + actualRecordSize + ")"); + } + if (version == TileMetricsVersion.THREE) { + this.density = UnsignedTypeUtil.uIntToFloat(header.getInt()); } } @@ -62,23 +65,38 @@ public IlluminaTileMetrics next() { if(!hasNext()) { throw new NoSuchElementException(); } - return new IlluminaTileMetrics(bbIterator.next()); + return new IlluminaTileMetrics(bbIterator.next(), version); } public void remove() { throw new UnsupportedOperationException(); } + public float getDensity() { + return density; + } + /** * IlluminaPhasingMetrics corresponds to a single record in a TileMetricsOut file */ public static class IlluminaTileMetrics { private final IlluminaLaneTileCode laneTileCode; private final float metricValue; - - public IlluminaTileMetrics(final ByteBuffer bb) { - this(UnsignedTypeUtil.uShortToInt(bb.getShort()), UnsignedTypeUtil.uShortToInt(bb.getShort()), - UnsignedTypeUtil.uShortToInt(bb.getShort()), bb.getFloat()); + private float metricValue2; + private byte type; + + public IlluminaTileMetrics(final ByteBuffer bb, TileMetricsVersion version) { + if (version == TileMetricsVersion.THREE) { + this.laneTileCode = new IlluminaLaneTileCode(UnsignedTypeUtil.uShortToInt(bb.getShort()), bb.getInt(), 0); + //need to dump 9 bytes + this.type = bb.get(); + this.metricValue = bb.getFloat(); + this.metricValue2 = bb.getFloat(); + } else { + this.laneTileCode = new IlluminaLaneTileCode(UnsignedTypeUtil.uShortToInt(bb.getShort()), UnsignedTypeUtil.uShortToInt(bb.getShort()), + UnsignedTypeUtil.uShortToInt(bb.getShort())); + this.metricValue = bb.getFloat(); + } } public IlluminaTileMetrics(final int laneNumber, final int tileNumber, final int metricCode, final float metricValue) { @@ -120,6 +138,10 @@ public boolean equals(final Object o) { public int hashCode() { return String.format("%s:%s:%s:%s", laneTileCode.getLaneNumber(), laneTileCode.getTileNumber(), laneTileCode.getMetricCode(), metricValue).hashCode(); // Slow but adequate. } + + public boolean isClusterRecord() { + return type == 't'; + } } /** Helper class which captures the combination of a lane, tile & metric code */ @@ -164,4 +186,19 @@ public int hashCode() { return result; } } + + public enum TileMetricsVersion { + TWO(2, 2, 10), + THREE(3, 6, 15); + + private final int version; + private final int headerSize; + private final int recordSize; + + TileMetricsVersion(int version, int headerSize, int recordSize) { + this.version = version; + this.headerSize = headerSize; + this.recordSize = recordSize; + } + } } diff --git a/src/main/java/picard/illumina/quality/CollectHiSeqXPfFailMetrics.java b/src/main/java/picard/illumina/quality/CollectHiSeqXPfFailMetrics.java index 77eb60c59..17dd6fe5c 100644 --- a/src/main/java/picard/illumina/quality/CollectHiSeqXPfFailMetrics.java +++ b/src/main/java/picard/illumina/quality/CollectHiSeqXPfFailMetrics.java @@ -32,8 +32,8 @@ import picard.cmdline.Option; import picard.cmdline.StandardOptionDefinitions; import picard.cmdline.programgroups.Metrics; +import picard.illumina.parser.BaseIlluminaDataProvider; import picard.illumina.parser.ClusterData; -import picard.illumina.parser.IlluminaDataProvider; import picard.illumina.parser.IlluminaDataProviderFactory; import picard.illumina.parser.IlluminaDataType; import picard.illumina.parser.ReadData; @@ -294,7 +294,7 @@ protected int doWork() { private final PFFailSummaryMetric summaryMetric; final Collection detailedMetrics; private Exception exception = null; - private final IlluminaDataProvider provider; + private final BaseIlluminaDataProvider provider; final private double pWriteDetailed; final private Random random = new Random(); diff --git a/src/main/java/picard/util/UnsignedTypeUtil.java b/src/main/java/picard/util/UnsignedTypeUtil.java index be382ad67..536cba6a7 100644 --- a/src/main/java/picard/util/UnsignedTypeUtil.java +++ b/src/main/java/picard/util/UnsignedTypeUtil.java @@ -25,4 +25,8 @@ public static int uShortToInt(final short unsignedShort) { public static long uIntToLong(final int unsignedInt) { return unsignedInt & 0xFFFFFFFFL; } + + public static float uIntToFloat(final int unsignedInt) { + return Float.intBitsToFloat(unsignedInt); + } } diff --git a/src/test/java/picard/illumina/ExtractIlluminaBarcodesTest.java b/src/test/java/picard/illumina/ExtractIlluminaBarcodesTest.java index 748043e68..1d92498f5 100644 --- a/src/test/java/picard/illumina/ExtractIlluminaBarcodesTest.java +++ b/src/test/java/picard/illumina/ExtractIlluminaBarcodesTest.java @@ -31,8 +31,8 @@ import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import picard.cmdline.CommandLineProgramTest; +import picard.illumina.parser.BaseIlluminaDataProvider; import picard.illumina.parser.ClusterData; -import picard.illumina.parser.IlluminaDataProvider; import picard.illumina.parser.IlluminaDataProviderFactory; import picard.illumina.parser.IlluminaDataType; import picard.illumina.parser.ReadStructure; @@ -117,7 +117,7 @@ public void testSingleEndWithBarcodeAtEnd() throws Exception { } @Test - public void testSingleEndWithBarcodeAtEndAndMolecularIndicies() throws Exception { + public void testSingleEndWithBarcodeAtEndAndMolecularIndicies() throws Exception { final MetricsFile metricsFile = runIt(1, "4M21T8B"); Assert.assertEquals(metricsFile.getMetrics().get(0).PERFECT_MATCHES, 5); } @@ -161,8 +161,7 @@ public void testNonWritableOutputFile() throws Exception { args.add("BARCODE=" + barcode); } Assert.assertEquals(runPicardCommandLine(args), 4); - } - finally { + } finally { existingFile.setWritable(true); } @@ -241,7 +240,7 @@ public void testDualBarcodes() throws Exception { final File metricsFile = File.createTempFile("dual.", ".metrics"); metricsFile.deleteOnExit(); - final String[] args = new String[] { + final String[] args = new String[]{ "BASECALLS_DIR=" + dual.getAbsolutePath(), "LANE=" + 1, "METRICS_FILE=" + metricsFile.getPath(), @@ -250,7 +249,7 @@ public void testDualBarcodes() throws Exception { }; Assert.assertEquals(runPicardCommandLine(args), 0); - final MetricsFile result = new MetricsFile(); + final MetricsFile result = new MetricsFile(); result.read(new FileReader(metricsFile)); Assert.assertEquals(result.getMetrics().get(0).PERFECT_MATCHES, 1, "Got wrong number of perfect matches"); Assert.assertEquals(result.getMetrics().get(0).ONE_MISMATCH_MATCHES, 0, "Got wrong number of one-mismatch matches"); @@ -266,7 +265,7 @@ public void testQualityBarcodes(final int quality, final File metricsFile = File.createTempFile("qual.", ".metrics"); metricsFile.deleteOnExit(); - final String[] args = new String[] { + final String[] args = new String[]{ "BASECALLS_DIR=" + qual.getPath(), "LANE=" + 1, "READ_STRUCTURE=25T8B25T", @@ -277,7 +276,7 @@ public void testQualityBarcodes(final int quality, }; Assert.assertEquals(runPicardCommandLine(args), 0); - final MetricsFile result = new MetricsFile(); + final MetricsFile result = new MetricsFile(); result.read(new FileReader(metricsFile)); Assert.assertEquals(result.getMetrics().get(0).PERFECT_MATCHES, perfectMatches, "Got wrong number of perfect matches for test: '" + testName + "'"); Assert.assertEquals(result.getMetrics().get(0).ONE_MISMATCH_MATCHES, oneMismatch, "Got wrong number of one-mismatch matches for test: '" + testName + "'"); @@ -285,7 +284,7 @@ public void testQualityBarcodes(final int quality, @DataProvider(name = "qualityBarcodeData") public Object[][] getQualityTestData() { - return new Object[][] { + return new Object[][]{ {16, 0, 1, 0, "Barcode has good quality, 1 match"}, {25, 0, 0, 0, "Barcode has quality failures, no matches"} }; @@ -295,11 +294,11 @@ private void testParsing(final IlluminaDataProviderFactory factory, final ReadSt int numReads = 0; - final IlluminaDataProvider dataProvider = factory.makeDataProvider(); + final BaseIlluminaDataProvider dataProvider = factory.makeDataProvider(); while (dataProvider.hasNext()) { final ClusterData cluster = dataProvider.next(); - if(metricACAGTG.BARCODE.equals(cluster.getMatchedBarcode())) { + if (metricACAGTG.BARCODE.equals(cluster.getMatchedBarcode())) { ++numReads; } @@ -331,7 +330,7 @@ private void testParsing(final IlluminaDataProviderFactory factory, final ReadSt // Generate _barcode.txt files and metrics file. Assert.assertEquals(runPicardCommandLine(args), 0); - final MetricsFile retval = new MetricsFile(); + final MetricsFile retval = new MetricsFile(); retval.read(new FileReader(metricsFile)); return retval; } diff --git a/src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java b/src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java index b2e431b35..16184f5c8 100644 --- a/src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java +++ b/src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java @@ -23,17 +23,21 @@ */ package picard.illumina; +import htsjdk.samtools.fastq.FastqReader; +import htsjdk.samtools.fastq.FastqRecord; import htsjdk.samtools.util.BufferedLineReader; import htsjdk.samtools.util.IOUtil; import htsjdk.samtools.util.LineReader; import htsjdk.samtools.util.StringUtil; import htsjdk.samtools.util.TestUtil; +import org.testng.Assert; import org.testng.annotations.Test; import picard.cmdline.CommandLineProgramTest; import picard.illumina.parser.ReadStructure; import java.io.File; import java.io.FileInputStream; +import java.io.FileNotFoundException; import java.io.PrintWriter; import java.util.ArrayList; import java.util.Arrays; @@ -46,8 +50,10 @@ private static final File TEST_DATA_DIR = new File("testdata/picard/illumina/25T8B25T/fastq"); private static final File TEST_DATA_DIR_WITH_4M = new File("testdata/picard/illumina/25T8B25T/fastq_with_4M"); private static final File TEST_DATA_DIR_WITH_4M4M = new File("testdata/picard/illumina/25T8B25T/fastq_with_4M4M"); + private static final File TEST_DATA_DIR_WITH_CBCLS = new File("testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls"); private static final File DUAL_TEST_DATA_DIR = new File("testdata/picard/illumina/25T8B8B25T/fastq"); + private static final File DUAL_CBCL_TEST_DATA_DIR = new File("testdata/picard/illumina/125T8B8B125T_cbcl/fastq"); public String getCommandLineProgramName() { return IlluminaBasecallsToFastq.class.getSimpleName(); @@ -100,8 +106,8 @@ public void testMultiplexWithIlluminaReadNameHeaders() throws Exception { }); final String[] filenames = new String[]{ - filePrefix + ".1.fastq", - filePrefix + ".barcode_1.fastq" + filePrefix + ".1.fastq", + filePrefix + ".barcode_1.fastq" }; for (final String filename : filenames) { IOUtil.assertFilesEqual(new File(outputDir, filename), new File(TEST_DATA_DIR, filename)); @@ -132,18 +138,86 @@ public void testDualBarcodes() throws Exception { runStandardTest(1, "dualBarcode.", "barcode_double.params", 2, "25T8B8B25T", DUAL_BASECALLS_DIR, DUAL_TEST_DATA_DIR); } + @Test + public void testCbclConvert() throws Exception { + runNewConverterTest(1, "dualBarcode.", "barcode_double.params", 2, "151T8B8B151T", TEST_DATA_DIR_WITH_CBCLS, DUAL_CBCL_TEST_DATA_DIR); + } + + private void runNewConverterTest(final int lane, final String jobName, final String libraryParamsFile, + final int concatNColumnFields, final String readStructureString, final File baseCallsDir, + final File testDataDir) throws Exception { + final File outputDir = File.createTempFile(jobName, ".dir"); + try { + outputDir.delete(); + outputDir.mkdir(); + + outputDir.deleteOnExit(); + // Create barcode.params with output files in the temp directory + final File libraryParams = new File(outputDir, libraryParamsFile); + libraryParams.deleteOnExit(); + final List outputPrefixes = new ArrayList(); + convertParamsFile(libraryParamsFile, concatNColumnFields, testDataDir, outputDir, libraryParams, outputPrefixes); + + runPicardCommandLine(new String[]{ + "BASECALLS_DIR=" + baseCallsDir, + "LANE=" + lane, + "RUN_BARCODE=HiMom", + "READ_STRUCTURE=" + readStructureString, + "MULTIPLEX_PARAMS=" + libraryParams, + "MACHINE_NAME=machine1", + "FLOWCELL_BARCODE=abcdeACXX", + "USE_NEW_CONVERTER=true", + "NUM_PROCESSORS=2", + "METRICS_FILE=" + new File(outputDir, "test.metrics") + }); + + final ReadStructure readStructure = new ReadStructure(readStructureString); + for (final File outputSam : outputPrefixes) { + for (int i = 1; i <= readStructure.templates.length(); ++i) { + final String filename = outputSam.getName() + "." + i + ".fastq"; + compareFastqs(testDataDir, outputSam, filename); + } + for (int i = 1; i <= readStructure.sampleBarcodes.length(); ++i) { + final String filename = outputSam.getName() + ".barcode_" + i + ".fastq"; + compareFastqs(testDataDir, outputSam, filename); + } + for (int i = 1; i <= readStructure.molecularBarcode.length(); ++i) { + final String filename = outputSam.getName() + ".index_" + i + ".fastq"; + compareFastqs(testDataDir, outputSam, filename); + } + } + + } finally { + TestUtil.recursiveDelete(outputDir); + } + } + + private void compareFastqs(File testDataDir, File outputSam, String filename) { + File f1 = new File(outputSam.getParentFile(), filename); + File f2 = new File(testDataDir, filename); + FastqReader reader1 = new FastqReader(f1); + List reads = new ArrayList<>(); + FastqReader reader2 = new FastqReader(f2); + for (FastqRecord record : reader1) { + reads.add(record); + } + + for (FastqRecord record : reader2) { + Assert.assertTrue(reads.contains(record)); + } + } + /** * This test utility takes a libraryParamsFile and generates output sam files through IlluminaBasecallsToFastq to compare against * preloaded test data * - * @param lane lane number to use - * @param jobName name of job for the temp file - * @param libraryParamsFile the params file to use for the de-multiplexing + * @param lane lane number to use + * @param jobName name of job for the temp file + * @param libraryParamsFile the params file to use for the de-multiplexing * @param concatNColumnFields how many columns to concatenate to get the barcode * @param readStructureString what read-structure string to use - * @param baseCallsDir what directory can I find the BCLs in - * @param testDataDir what directory can I find the expected resulting files - * + * @param baseCallsDir what directory can I find the BCLs in + * @param testDataDir what directory can I find the expected resulting files * @throws Exception */ @@ -160,22 +234,8 @@ private void runStandardTest(final int lane, final String jobName, final String final File libraryParams = new File(outputDir, libraryParamsFile); libraryParams.deleteOnExit(); final List outputPrefixes = new ArrayList(); - final LineReader reader = new BufferedLineReader(new FileInputStream(new File(testDataDir, libraryParamsFile))); - final PrintWriter writer = new PrintWriter(libraryParams); - final String header = reader.readLine(); - writer.println(header + "\tOUTPUT_PREFIX"); - while (true) { - final String line = reader.readLine(); - if (line == null) { - break; - } - final String[] fields = line.split("\t"); - final File outputPrefix = new File(outputDir, StringUtil.join("", Arrays.copyOfRange(fields, 0, concatNColumnFields))); - outputPrefixes.add(outputPrefix); - writer.println(line + "\t" + outputPrefix); - } - writer.close(); - reader.close(); + convertParamsFile(libraryParamsFile, concatNColumnFields, testDataDir, outputDir, libraryParams, outputPrefixes); + runPicardCommandLine(new String[]{ "BASECALLS_DIR=" + baseCallsDir, @@ -207,4 +267,23 @@ private void runStandardTest(final int lane, final String jobName, final String TestUtil.recursiveDelete(outputDir); } } + + private void convertParamsFile(String libraryParamsFile, int concatNColumnFields, File testDataDir, File outputDir, File libraryParams, List outputPrefixes) throws FileNotFoundException { + try (LineReader reader = new BufferedLineReader(new FileInputStream(new File(testDataDir, libraryParamsFile)))) { + final PrintWriter writer = new PrintWriter(libraryParams); + final String header = reader.readLine(); + writer.println(header + "\tOUTPUT_PREFIX"); + while (true) { + final String line = reader.readLine(); + if (line == null) { + break; + } + final String[] fields = line.split("\t"); + final File outputPrefix = new File(outputDir, StringUtil.join("", Arrays.copyOfRange(fields, 0, concatNColumnFields))); + outputPrefixes.add(outputPrefix); + writer.println(line + "\t" + outputPrefix); + } + writer.close(); + } + } } diff --git a/src/test/java/picard/illumina/IlluminaBasecallsToSamTest.java b/src/test/java/picard/illumina/IlluminaBasecallsToSamTest.java index 63d4e799c..f7a0d6a2f 100644 --- a/src/test/java/picard/illumina/IlluminaBasecallsToSamTest.java +++ b/src/test/java/picard/illumina/IlluminaBasecallsToSamTest.java @@ -52,6 +52,8 @@ private static final File DUAL_TEST_DATA_DIR = new File("testdata/picard/illumina/25T8B8B25T/sams"); private static final File TEST_DATA_DIR_WITH_4M_INDEX = new File("testdata/picard/illumina/25T8B25T/sams_with_4M"); private static final File TEST_DATA_DIR_WITH_4M4M_INDEX = new File("testdata/picard/illumina/25T8B25T/sams_with_4M4M"); + private static final File TEST_DATA_DIR_WITH_CBCLS = new File("testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls"); + private static final File DUAL_CBCL_TEST_DATA_DIR = new File("testdata/picard/illumina/125T8B8B125T_cbcl/sams"); public String getCommandLineProgramName() { return IlluminaBasecallsToSam.class.getSimpleName(); @@ -252,6 +254,54 @@ public void testDualBarcodes() throws Exception { runStandardTest(1, "dualBarcode.", "barcode_double.params", 1, "25T8B8B25T", DUAL_BASECALLS_DIR, DUAL_TEST_DATA_DIR); } + @Test + public void testCbclConvert() throws Exception { + runNewConverterTest(1, "dualBarcode.", "barcode_double.params", 2, "151T8B8B151T", TEST_DATA_DIR_WITH_CBCLS, DUAL_CBCL_TEST_DATA_DIR); + } + + private void runNewConverterTest(final int lane, final String jobName, final String libraryParamsFile, + final int concatNColumnFields, final String readStructure, final File baseCallsDir, + final File testDataDir) throws Exception { + final File outputDir = File.createTempFile(jobName, ".dir"); + outputDir.delete(); + outputDir.mkdir(); + outputDir.deleteOnExit(); + // Create barcode.params with output files in the temp directory + final File libraryParams = new File(outputDir, libraryParamsFile); + libraryParams.deleteOnExit(); + final List samFiles = new ArrayList(); + final LineReader reader = new BufferedLineReader(new FileInputStream(new File(testDataDir, libraryParamsFile))); + final PrintWriter writer = new PrintWriter(libraryParams); + final String header = reader.readLine(); + writer.println(header + "\tOUTPUT"); + while (true) { + final String line = reader.readLine(); + if (line == null) { + break; + } + final String[] fields = line.split("\t"); + final File outputSam = new File(outputDir, StringUtil.join("", Arrays.copyOfRange(fields, 0, concatNColumnFields)) + ".sam"); + outputSam.deleteOnExit(); + samFiles.add(outputSam); + writer.println(line + "\t" + outputSam); + } + writer.close(); + reader.close(); + + Assert.assertEquals(runPicardCommandLine(new String[]{ + "BASECALLS_DIR=" + baseCallsDir, + "LANE=" + lane, + "RUN_BARCODE=HiMom", + "READ_STRUCTURE=" + readStructure, + "LIBRARY_PARAMS=" + libraryParams, + "USE_NEW_CONVERTER=true" + }), 0); + + for (final File outputSam : samFiles) { + IOUtil.assertFilesEqual(outputSam, new File(testDataDir, outputSam.getName())); + } + TestUtil.recursiveDelete(outputDir); + } /** * Ensures that a run missing a barcode from the parameters file throws an error. * diff --git a/src/test/java/picard/illumina/IlluminaLaneMetricsCollectorTest.java b/src/test/java/picard/illumina/IlluminaLaneMetricsCollectorTest.java index bf6b86d0d..030865c01 100644 --- a/src/test/java/picard/illumina/IlluminaLaneMetricsCollectorTest.java +++ b/src/test/java/picard/illumina/IlluminaLaneMetricsCollectorTest.java @@ -2,15 +2,13 @@ import htsjdk.samtools.ValidationStringency; import htsjdk.samtools.util.IOUtil; -import picard.PicardException; -import picard.illumina.parser.ReadStructure; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; +import picard.PicardException; +import picard.illumina.parser.ReadStructure; import java.io.File; import java.io.IOException; -import java.lang.Exception;import java.lang.Object;import java.lang.String; -import java.nio.file.Files; import java.util.Arrays; /** @author mccowan */ @@ -52,13 +50,14 @@ public void testWriteLaneMetrics(final String testRun) throws Exception { } @Test(dataProvider = "testCollectIlluminaLaneMetrics") - public void testCollectIlluminaLaneMetrics(final String testRun, final ReadStructure readStructure) throws Exception { + public void testCollectIlluminaLaneMetrics(final String testRun, final ReadStructure readStructure, final boolean isNovaSeq) throws Exception { for (final boolean useReadStructure : Arrays.asList(true, false)) { final File runDirectory = new File(TILE_RUN_DIRECTORY, testRun); final CollectIlluminaLaneMetrics clp = new CollectIlluminaLaneMetrics(); clp.OUTPUT_DIRECTORY = IOUtil.createTempDir("illuminaLaneMetricsCollectorTest", null); clp.RUN_DIRECTORY = runDirectory; clp.OUTPUT_PREFIX = "test"; + clp.IS_NOVASEQ = isNovaSeq; if (useReadStructure) clp.READ_STRUCTURE = readStructure; clp.doWork(); @@ -76,11 +75,12 @@ public void testCollectIlluminaLaneMetrics(final String testRun, final ReadStruc @DataProvider(name = "testCollectIlluminaLaneMetrics") public Object[][] testCollectIlluminaLaneMetricsDataProvider() { return new Object[][] { - {"A7LE0", new ReadStructure("25T8B8B25T")}, - {"C2MFAACXX", new ReadStructure("95T101T")}, - {"H7BATADXX", new ReadStructure("76T8B76T")}, - {"H7H7RADXX", new ReadStructure("101T8B8B101T")}, - {"A67HY", new ReadStructure("8B8B")} + {"A7LE0", new ReadStructure("25T8B8B25T"), false}, + {"C2MFAACXX", new ReadStructure("95T101T"), false}, + {"H7BATADXX", new ReadStructure("76T8B76T"), false}, + {"H7H7RADXX", new ReadStructure("101T8B8B101T"), false}, + {"A67HY", new ReadStructure("8B8B"), false}, + {"NovaSeq", new ReadStructure("151T8B8B151T"), true} }; } diff --git a/src/test/java/picard/illumina/parser/IlluminaDataProviderTest.java b/src/test/java/picard/illumina/parser/IlluminaDataProviderTest.java index de4cf0a88..33b36dd3d 100644 --- a/src/test/java/picard/illumina/parser/IlluminaDataProviderTest.java +++ b/src/test/java/picard/illumina/parser/IlluminaDataProviderTest.java @@ -53,7 +53,7 @@ private void runTest( final String testName, final int size, final Map readNoToClusterData, final int seekAfterFirstRead, final int seekTestDataReadOffset, - final IlluminaDataProvider dataProvider) + final BaseIlluminaDataProvider dataProvider) throws Exception { int count = 0; @@ -116,7 +116,7 @@ private void compareReadData(final ClusterData cd1, final ClusterData cd2, final public void runBarcodeParsingTest(final IlluminaDataProviderFactory factory) { int total = 0; - final IlluminaDataProvider dataProvider = factory.makeDataProvider(); + final BaseIlluminaDataProvider dataProvider = factory.makeDataProvider(); while (dataProvider.hasNext()) { final ClusterData cluster = dataProvider.next(); final String matchedBarcode = cluster.getMatchedBarcode(); @@ -197,7 +197,7 @@ public void testIlluminaDataProviderBclMethod( final Map readNoToClusterData = BinTdUtil.clusterData(lane, tiles, illuminaConfigStr, dts); final IlluminaDataProviderFactory factory = new IlluminaDataProviderFactory(basecallsDirectory, lane, new ReadStructure(illuminaConfigStr), bclQualityEvaluationStrategy, dts); - final IlluminaDataProvider dataProvider = factory.makeDataProvider(); + final BaseIlluminaDataProvider dataProvider = factory.makeDataProvider(); runTest(testName, size, readNoToClusterData, seekAfterFirstRead, seekTestDataReadOffset, dataProvider); } diff --git a/src/test/java/picard/illumina/parser/readers/CbclReaderTest.java b/src/test/java/picard/illumina/parser/readers/CbclReaderTest.java index 80f9956f8..15529ea41 100644 --- a/src/test/java/picard/illumina/parser/readers/CbclReaderTest.java +++ b/src/test/java/picard/illumina/parser/readers/CbclReaderTest.java @@ -7,31 +7,33 @@ import java.io.File; import java.util.Arrays; import java.util.HashMap; +import java.util.List; import java.util.Map; public class CbclReaderTest { - public static final File TestDataDir = new File("testdata/picard/illumina/readerTests"); - public static final File PASSING_CBCL_C99_1 = new File(TestDataDir, "C99.1.cbcl"); - public static final File PASSING_CBCL_C100_1 = new File(TestDataDir, "C100.1.cbcl"); + public static final File TestDataDir = new File("testdata/picard/illumina/readerTests/cbcls"); + public static final File PASSING_CBCL_C99_1 = new File(TestDataDir + "/C1.1", "L001_1.cbcl"); + public static final File PASSING_CBCL_C100_1 = new File(TestDataDir + "/C2.1", "L001_1.cbcl"); public static final File TILE_1101_FILTER = new File(TestDataDir, "tile_1101.filter"); - public static final File TILE_1102_FILTER = new File(TestDataDir, "tile_1102.filter"); public static final char[] expectedBases = new char[]{ - 'G','G','C','C','G','A','A','G','T','A','C','C','C','T','G','A' + 'G', 'G', 'C', 'C', 'G', 'A', 'A', 'G' }; public static final int[] expectedQuals = new int[]{ - 37,37,37,37,37,37,37,12,37,37,37,37,37,37,12,37 + 37, 37, 37, 37, 37, 37, 37, 12 }; @Test public void testReadValidFile() { - final CbclReader reader = new CbclReader(Arrays.asList(PASSING_CBCL_C99_1, PASSING_CBCL_C100_1), new int[] {2}); Map filters = new HashMap<>(); filters.put(1101, TILE_1101_FILTER); - filters.put(1102, TILE_1102_FILTER); - reader.addFilters(filters); + LocsFileReader locsFileReader = new LocsFileReader(new File("testdata/picard/illumina/readerTests/s_1_6.locs")); + List locs = locsFileReader.toList(); + + final CbclReader reader = new CbclReader(Arrays.asList(PASSING_CBCL_C99_1, PASSING_CBCL_C100_1), + filters, new int[]{2}, 1101, locs, false); int i = 0; while (reader.hasNext()) { @@ -39,7 +41,7 @@ public void testReadValidFile() { for (int cluster = 0; cluster < bv.bases.length; cluster++) { for (int cycle = 0; cycle < bv.bases[cluster].length; cycle++) { String actual = new String(new byte[]{bv.bases[cluster][cycle]}); - String expected = new String(new char[]{expectedBases[i]}); + String expected = new String(new char[]{expectedBases[i]}); Assert.assertEquals(actual, expected, "For cluster " + cluster + " cycle " + cycle + ","); Assert.assertEquals(bv.qualities[cluster][cycle], expectedQuals[i], "For cluster " + cluster + " cycle " + cycle + ","); i++; diff --git a/src/test/java/picard/util/FifoBufferTest.java b/src/test/java/picard/util/FifoBufferTest.java index 41b2cc5e6..75fb180a2 100644 --- a/src/test/java/picard/util/FifoBufferTest.java +++ b/src/test/java/picard/util/FifoBufferTest.java @@ -58,8 +58,8 @@ public void test(final double megabytes) throws IOException { } // Run the input file through the FifoBuffer and back into another file - final Md5CalculatingInputStream in = new Md5CalculatingInputStream(new FileInputStream(inputFile), (File)null); - final Md5CalculatingOutputStream out = new Md5CalculatingOutputStream(new FileOutputStream("/dev/null"), (File)null); + final Md5CalculatingInputStream in = new Md5CalculatingInputStream(new FileInputStream(inputFile), (File) null); + final Md5CalculatingOutputStream out = new Md5CalculatingOutputStream(new FileOutputStream("/dev/null"), (File) null); final PrintStream outStream = new PrintStream(out); final FifoBuffer buffer = new FifoBuffer(in, outStream); buffer.BUFFER_SIZE = 128 * 1024 * 1024; diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C1.1/L001_1.cbcl b/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C1.1/L001_1.cbcl new file mode 100644 index 000000000..53fbfb60a Binary files /dev/null and b/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C1.1/L001_1.cbcl differ diff --git 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b/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/s_1_1101.filter new file mode 100755 index 000000000..76adc5004 Binary files /dev/null and b/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/s_1_1101.filter differ diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/s_1_1102.filter b/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/s_1_1102.filter new file mode 100755 index 000000000..76adc5004 Binary files /dev/null and b/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/s_1_1102.filter differ diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/s.locs b/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/s.locs new file mode 100755 index 000000000..2db736ff7 Binary files /dev/null and b/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/s.locs differ diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CACCTAGTACTCGAGT.1.fastq b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CACCTAGTACTCGAGT.1.fastq new file mode 100644 index 000000000..d501ec2b8 --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CACCTAGTACTCGAGT.1.fastq @@ -0,0 +1,4 @@ +@machine1:HiMom:abcdeACXX:1:1101:1271:1000 1:N:0:CACCTAGTACTCGAGT +GANGTCTCGTTTATCGGGGCATTTTCTTGACTGCGTTAGCATGGTTCTCGTGCACGTATTCGTTGTCTGCTCTCTACTGCTCTTCTATGGTACAACTTCTTCATGTACNAGTATCCCTTGANGGNGCCCCACTCCAACGNCTTGTAAAGAT ++ +!8#!--!F!88!8---F!F--!88F-!FFFFF88F-8888FF!F8888--F-F--FFF88!8!!8F!8!--F!-!FF-!8F---!88--8!F-8-8F8F-!F8F!88!#FF-F-FF-!F!F#!8#--!-8-8F8!-8-!#!--!!-88FFF diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CACCTAGTACTCGAGT.2.fastq b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CACCTAGTACTCGAGT.2.fastq new file mode 100644 index 000000000..8577e7db1 --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CACCTAGTACTCGAGT.2.fastq @@ -0,0 +1,4 @@ +@machine1:HiMom:abcdeACXX:1:1101:1271:1000 2:N:0:CACCTAGTACTCGAGT +TGATGGTANCTANTCNNTCCCCGCTATGCCGACTGCATATAGTGTGCGCACAAGCACAGGTTTGGTNNCTATTTGTNNTATCCGTCCCCTCTATCNTTGGNGNTGTAATGTGCGGCCTGCTCTCTATAGCGTAGCCTAGTNGGTCTGCGTT ++ +FF88--!8#F!-#!F##F-888!!-F8F8!FF--8!F!8-8!F888!88F!F8-8F!8F!F8F-!F##8!F8FFF-##8F--F88888F!8!888#88!F#F#8FF--8--F-FFFF--F-F-F8F8F8--!8!!F88F8#88FFF-8!8- diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CACCTAGTACTCGAGT.barcode_1.fastq b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CACCTAGTACTCGAGT.barcode_1.fastq new file mode 100644 index 000000000..3cd7d7a91 --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CACCTAGTACTCGAGT.barcode_1.fastq @@ -0,0 +1,4 @@ +@machine1:HiMom:abcdeACXX:1:1101:1271:1000 :N:0:CACCTAGTACTCGAGT +CACCTAGT ++ +--F!F-F- diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CACCTAGTACTCGAGT.barcode_2.fastq b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CACCTAGTACTCGAGT.barcode_2.fastq new file mode 100644 index 000000000..decb20468 --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CACCTAGTACTCGAGT.barcode_2.fastq @@ -0,0 +1,4 @@ +@machine1:HiMom:abcdeACXX:1:1101:1271:1000 :N:0:CACCTAGTACTCGAGT +ACTCGAGT ++ +8--F--F- diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CCCCGCTTTTGCGTGT.1.fastq b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CCCCGCTTTTGCGTGT.1.fastq new file mode 100644 index 000000000..557bdb078 --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CCCCGCTTTTGCGTGT.1.fastq @@ -0,0 +1,4 @@ +@machine1:HiMom:abcdeACXX:1:1102:1325:1000 1:N:0:CCCCGCTTTTGCGTGT +GNTGGCCTGCATGAATTGANCATNAAAGNGGGTCCCGTAGGNANCNTACNGAACATTAGTGCAGTTTNGNCCACNGTGANGCGGNAGGCGGAAGGTNATTNTTAACCTCCCCCTGTNTGTACTGATGATCGGGGGGGCANCCGGATGCGAT ++ +-#-8-!!!88FF-8F!-8F#F-!#F---#8!F--8FFFFF!#8#!#---#--88--F8-8-8F888F#!#FFF8#!88F#FF!!#8F-!F!88!8F#8-!#88F88!!FF!F888!#!F!--888888----F8-888F#F8!--F-!-8! diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CCCCGCTTTTGCGTGT.2.fastq b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CCCCGCTTTTGCGTGT.2.fastq new file mode 100644 index 000000000..da56cf7e3 --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CCCCGCTTTTGCGTGT.2.fastq @@ -0,0 +1,4 @@ +@machine1:HiMom:abcdeACXX:1:1102:1325:1000 2:N:0:CCCCGCTTTTGCGTGT +ACGCCGTTGTGCGCTATTAACGCCNCTACACAATACCCNTCGTATTCTCCAGGGNACGTTGTGGCNGGGTACCCAGAGGTGGGTATGGTTGTTGGATACAGTGGGGGNCGGCTTCGNTGGTCCCCTTACCGGAGGACCAACGAACCACCCG ++ +88F8FF-F88F8F!8888F88-8F#!!F88-8F!888!#!8--8---FFFFF-F#8-8!-F!---#-!-F8-----8!F!!F-8F!!8!!8-!!!F!-8-FF8!F-8#8-F---F8#!F-8-8----8F888-!!FF!F8-!F88F8FFFF diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CCCCGCTTTTGCGTGT.barcode_1.fastq b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CCCCGCTTTTGCGTGT.barcode_1.fastq new file mode 100644 index 000000000..f22d51ce0 --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CCCCGCTTTTGCGTGT.barcode_1.fastq @@ -0,0 +1,4 @@ +@machine1:HiMom:abcdeACXX:1:1102:1325:1000 :N:0:CCCCGCTTTTGCGTGT +CCCCGCTT ++ +FF8!FF!! diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CCCCGCTTTTGCGTGT.barcode_2.fastq b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CCCCGCTTTTGCGTGT.barcode_2.fastq new file mode 100644 index 000000000..54bcd88d8 --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/CCCCGCTTTTGCGTGT.barcode_2.fastq @@ -0,0 +1,4 @@ +@machine1:HiMom:abcdeACXX:1:1102:1325:1000 :N:0:CCCCGCTTTTGCGTGT +TTGCGTGT ++ +FFF8!888 diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/GCTATAGTCCAGCAGC.1.fastq b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/GCTATAGTCCAGCAGC.1.fastq new file mode 100644 index 000000000..85efcfb0a --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/GCTATAGTCCAGCAGC.1.fastq @@ -0,0 +1,4 @@ +@machine1:HiMom:abcdeACXX:1:1101:1380:1000 1:N:0:GCTATAGTCCAGCAGC +GTTGCGCACGCGCGTGGGCNACGNNNCGGTATTCCAACATCCGTGGTGCANGTANAGTAGTATGGTNAAATATCCATCNCAGGCTTCGAATCGGGCTGTGGATGTCCAATNCNTTGTACGGCNACACTCTACCTACTACTACCCAGGCTGG ++ +F-F8-F888F8!F88F-!-#-F8###8!!F888--8-F888!8----8-8#F88#8--8FF88FF8#-8-F-8F8-8!#88F88-F888F-FF8F!!8-8-F---F!FFF#F#F-!-8!F8-#8-888--888!8F-8-88---FF!88FF diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/GCTATAGTCCAGCAGC.2.fastq b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/GCTATAGTCCAGCAGC.2.fastq new file mode 100644 index 000000000..1f4c058ed --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/GCTATAGTCCAGCAGC.2.fastq @@ -0,0 +1,4 @@ +@machine1:HiMom:abcdeACXX:1:1101:1380:1000 2:N:0:GCTATAGTCCAGCAGC +AATGTGGCCTCTAGNTNGAATTCNGCGGGTGAGGCGTACGTTTCAACGTAGCGAANGTNGGATGTTTGCCCANGACATNTTTCGATTGCNGTNCCTGTNACGATACGTTCCTGTCAGNNTGCGNAGCTGNGCGAATTCACNCTGCTGTCTG ++ +F8-F!F88FF-88-#!#F-F--F#F!--8-8-8!-8----!F!-F-8!FFF8!-8#8F#-F8!F!FF8-F!8#8F--F#FF!8!-!F8!#-F#8!F!!#F!F88-!8!!---8-FF!##-8!!#-F!-F#8888FFFF--#!F88!8!8-! diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/GCTATAGTCCAGCAGC.barcode_1.fastq b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/GCTATAGTCCAGCAGC.barcode_1.fastq new file mode 100644 index 000000000..95cddaa53 --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/GCTATAGTCCAGCAGC.barcode_1.fastq @@ -0,0 +1,4 @@ +@machine1:HiMom:abcdeACXX:1:1101:1380:1000 :N:0:GCTATAGTCCAGCAGC +GCTATAGT ++ +F8!8!-F8 diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/GCTATAGTCCAGCAGC.barcode_2.fastq b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/GCTATAGTCCAGCAGC.barcode_2.fastq new file mode 100644 index 000000000..5e5275ed4 --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/GCTATAGTCCAGCAGC.barcode_2.fastq @@ -0,0 +1,4 @@ +@machine1:HiMom:abcdeACXX:1:1101:1380:1000 :N:0:GCTATAGTCCAGCAGC +CCAGCAGC ++ +-8FF!FFF diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/NN.1.fastq b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/NN.1.fastq new file mode 100644 index 000000000..2e80ce48d --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/NN.1.fastq @@ -0,0 +1,184 @@ +@machine1:HiMom:abcdeACXX:1:1101:1000:1000 1:N:0: +TGATGGTTTCGGGNTTTAGACAGTGTCATGCCTATTCCNTGGTANTCTTTGTTAACCTACGCCTCATGCTCGAATTCGCGNGTNCAGGATAGAACTTAAAGNTCTTTGTCTGAGGCAGAGANCGGAAGNTTTTCAGCTGTGAGGTTCCCTT ++ +888-8F!!88-F8#!!F8FF!F-!--88!!FF8F--F!#-88F8#!!F!F!!8F88F88!!!8FFFF--F8FF88-8F88#!!#F-F88!------FFFFF#!8F!F8F-8---88-88F8#F!-F-8#!-!8--8!------F8---F!- +@machine1:HiMom:abcdeACXX:1:1101:1018:1000 1:N:0: +GGTGGGGCAGCTCNNGTNCTGGGTATGNTTACATGATTCAAGCATACTGCCCCTGATANTANTCGCGGNTTCTGCTANGTATTTCCCGGGAACTTCTTTCACCTATCCGAACAACAGCTTTCCCAGTCAGAGTCAGCGAACATTATAACTC ++ +FFF!-!-!F!!!!##!F#!FF8!FF-!#8!8F-8!----F-!-F8--88-FF!-!8F-#88#-8F!8F#88-8!!FF#!F8!8!!F!F-F-F!8F8FF!8---8-FFF8---8-8--!!-F8-!8888F8F8!F8FFF--!F!-8FFF--F +@machine1:HiMom:abcdeACXX:1:1101:1072:1000 1:N:0: +CCTTGATCNCTCCGCTTGAGTTTNGTTTCAGATGCCTTNAGGAAGCGATATTCCAACTCATGGAGCGTCAGCAGCGATTGTCGTATAGCCGGGCAAATCACTAGGAATGCCNTNTGTGAACAGTGGCATTGTTGTATGGTGTGTCCCCAAG ++ +-F-F88--#F8F888-!8F!F--#-!-F8--8!FF!-8#F8-F8-F88!-F8-8--!FF8FFF-F88!!F8!-!8--8-!!!-F--F!F----FFFF!-8!8-F-F-8F8!#-#--8F--88-!-!!88-!F-!FFFF8F8F8F!-88FF8 +@machine1:HiMom:abcdeACXX:1:1101:1090:1000 1:N:0: +GNATAGGNAANGGAGCNCCTGTAAAGTGCCGGTACATTGAATACCTCTCANATGNCAGAAGTAGACCAGCTTCGNCAGGACAAATTCATCATAGTTTATAGGTAATCCANTTGAGGCNCCTTGGCTTGATATTCTCCCGTCTACCGAGTCT ++ +F#F-F-!#-8#!8---#F8!!F8-F8F-!8-!8-!8!F!F-88F88-F--#FF-#--88-!8F--FFF!8-8!-#FFF8F88F-!!--!!F!8!--88F-F8F8--!--#88!F8-!#F!8!F88F-F-F-FF8FFF8F-!!F8-!-!F-8 +@machine1:HiMom:abcdeACXX:1:1101:1108:1000 1:N:0: +NTCTNANATTAAGTGCGGCAGNTGGGGCCCCCTGGTTTGAGTNAAATTGTGCGTCTATCTTACGCGGANGNAATGNCAGGACCGGGCGNCCTGTAGGGNATCANCCTATCTNCGAGTAAGTGAGGGGANATCGGTTCTCACGAATGCACGT ++ +#FFF#-#F!!8-88-!8F888#F--FF8!FF8!F-!88-88!#888!!8F--F-8!88-F-FF-F!8-#8#88-F#-FFFF8!-8--F#-88--8FFF#F8F-#F-8--8-#!-F-8-8-8-8-8FF-#8!!888-8-88888-!--8F-8 +@machine1:HiMom:abcdeACXX:1:1101:1127:1000 1:N:0: +TTTTCTTTGTTANGCCGTCNATGGGTCCNGGCCCACCGTACANACCCATCAGCGTCTGACGNCCGTACTTCGNTACTTATGGTGACTGTGANTGCCACGACTTGTCATNTACTTGGGGTTGTGANTANTACACCCTATCCGAACTTNAGGT ++ +F8F-8!-!F8-8#!FFFF-#FF--F8!8#8!F-8-!!--8!-#-F-88!8-!FF!FF8F8F#F-FF8!88-8#--8!F-F8--F-!8F888#!!--8!F8888!F!8!#88-F88!!-F!F8!8#88#F-8F!-F!8!8!!8F-F8#88FF +@machine1:HiMom:abcdeACXX:1:1101:1163:1000 1:N:0: +TCCTNCANTCGCACCGGAGAATTCCCACGATTCCCAAGCNAANACGATCTAATCTGAGCTTAGAACGAACAGACTCGGTAGGGGGATATTGTATCGCTGCCGTCGCGTGCTATGCTACGGTCTCNGTTATAATGGCNTTTTGGTCGCTTTA ++ +F8F8#-8#-8F88!F--88F8--!8!F8F8!!F!!FF-8#-F#FF--F!8888-F!--88-888-!F8F!8FF8--8!FF!888!8--F8F-F8F!-!8---88-F8F-!!F888-88F8!F88#F-FF8F-!!8-#!F!-!88-!F!888 +@machine1:HiMom:abcdeACXX:1:1101:1181:1000 1:N:0: +CGCGTGAAACGTCCACAATAGNGACGTCGCGTGATGTTGTTCTANGGCGATACNACGAGGTGATCAGAACNCCTTCAGTTTGTTGGAGTCNCTTCTGGACACCNCACCCGGATGATTAAGAGCTACGCGCTAGCCATATACGANATCCNTC ++ +!8-!88888-!F8!888F!8!#8--F!F!--!-F!-F-!8!F88#!-!----F#---F-8F!8!-8-8--#8-F!F88-!-!F8!!-!!F#8F--F8FF-8!-#-FF-FF8F!FF-!FF8-8---F!F8F888!!--FFF---#888!#!- +@machine1:HiMom:abcdeACXX:1:1101:1199:1000 1:N:0: +NACCCCNGGTGCTCAAAANTTGTAGTCTGGACTGAGNCGCGGAGACNTGGTGGTTGTCCACCGTCGNCTTCCGCTGGCGAATTCTCATATTNTGCNNCAGATACGGGTACCANGNATGTTGGTCAAANCCCTCGTCCCACGCGACNGAGAA ++ +#-F!FF#F!88!8!88-F#-!-F8-!F-8-F88!F8#-!F!F8---#8!--8-!!!!F8-FF8!8-#8F8-F8F-!!-F8F!-F8--!F-F#-!-##FF--!-F8-F!FF!-#-#FF-!888!FF8F#-F8---!8F!88!!8F8#8-88F +@machine1:HiMom:abcdeACXX:1:1101:1217:1000 1:N:0: +CCATCGTCAAGAGGTGCGTGGCACAAATATCGACTGATGTAGCATANGGACGATGTTCANGCGGTGGCTGCAAGAACACCTCCATCTGGGATATTCGTGTCTTTTNACGCGCGAATGGTTTCNCTACTGTCCACGTACACTTGCTTCACCA ++ +!---!!!F-888-!8---!8!88-FF88-F-FF8-8FF8-FFF--8#-!-8!FFFF!8F#F!FF!!F8-F--F!FF-FF!8!8F88!8!8F8F8-F-F-!!8!8-#-F8FFF!88!8-!-88#!FF-F8-!FF!8!8FF-F-8FF8-F-!8 +@machine1:HiMom:abcdeACXX:1:1101:1235:1000 1:N:0: +GGTTTAGGCCACGACNCGTTGCCGNGGGGTCGAGCTTTCTANTCATGGCTTTGTCATGTCGCTGCCATGGACGACAGTCCGGACTCGGGTCCGAGNGCNNGGGCGGTNCTCNGGCATCGAACCAGGTATCTAAGCGTNTCAGGCAATTCAG ++ +F-!-F8-8!F--F88#!F!-F8!!#!-!8!!FF!-FF8F-F#F8---88!!F8!!888-8888FFFFF-FF--FFF-F8--8FF!!8!-8!!---#!!##8-888!!#!-!#F8!F!!FF8--F-8!--F!---F-8#8F-8F-8--F-88 +@machine1:HiMom:abcdeACXX:1:1101:1253:1000 1:N:0: +NGTTGAGNAGTCCCTANTGAGGCATTTCCAATCNTTCGGTGGNCGCTTATCGGGTGGGGATTCGATCGGGAATCGCGCANCNCGTCAGTGTATGATTCNANATCGGTGCGTTCNTAACTTGGNCTATGTCCNCGACANCCTCGGTCTGCTT ++ +#!F-88F#8---F8F-#-F8F!-FF8!8!-88-#-8!F-F--#FF!!8-8F!8F!!F!F8F-88F!--8!8FF!F--!F#!#-F88F!8!F--!8FF8#8#F!-!!FF!-8-!#!-8!-F!!#!!88F8-F#-FFF-#F---!F!!F!!8! +@machine1:HiMom:abcdeACXX:1:1101:1289:1000 1:N:0: +TTCCGAGGCNCCGTACTTTTCTANCNCCCNCTNTGCGTGTTATGCGTAACGTGTCTGTTANTGNCCCGTGAATTAGGAGCGAGCTACTGATGAGGTCGTCCGGGGCGCANTAGACCCCCTTTTCTNCTAACCGNGAATGGTATGCCTGNCN ++ +8!!8-F-F8#!F8!-!F!8F88F#-#!--#-8#!--8-F!-8-8-!!8F!!F8F-!8F88#-!#8!8-888F!-8888!-F--8!8-F8-8F-!-88-8F8-8888---#!FF-!-!8FF-!8-!#FF-8!-F#F-8!8!FF!-F!-F#!# +@machine1:HiMom:abcdeACXX:1:1101:1307:1000 1:N:0: +GTNGTATGTACAGAGACTGTGTCGTTTAGTGGGGTTNGGAGCGGCCGNANTCTTGGCCGCGCNGNCCCTTGTTCTACCGGCAGCGTCAGCTCGTTTATCACCNACNGGAGTCTGCGACTTGTTAGGNCANTACCTATGAGAGCGCNCGCNG ++ +88#-8-8F!8!8F-888F!F-FF-!-F8-!8!8!-8#!-F8!!!8-!#F#-F8!FF!!-F!8#F#!!F8!FF-8--8F!-!FFF888FF!8F!!!-F-!8-F#88#---F!-F-8-FFF!8F-8FF#!-#F---8F!F8--88!!#8-!#! +@machine1:HiMom:abcdeACXX:1:1101:1325:1000 1:N:0: +AACGCCTTTGGATCCCCTCCACGGAGGTTACAGATTAGTAGNCAGGACNCNACNCGAAACGAGTGTTCTGTGAGGGTCATCNTAACGNTNCGNGCAATGGANACAAACAACAGGATTAATCGAGCTAACGNACCTNGATGGTAGCGAGCGG ++ +8--!F-8-!888FF!FF!!!8F-88F!-88---8F!--8--#F----!#!#F-#8--88--88!!!8!F88-F8-F-!F!8#-FF-!#F#-F#---FF!FF#----8-F88F!!8FF-8!---F-FF8F8#F-!F#8F!!8-F-!!8--88 +@machine1:HiMom:abcdeACXX:1:1101:1344:1000 1:N:0: +CACTTCTNGTTCACANGGGTAGCCCNTTGTTTCTTGTTNTTCGCATTGATCTTTTCCGGGTAGCCAATCANCGGTACGGCCCACGGCGTTTCATGTTAGAGTNTGGGGTACAACATCCCTACGCTGTCCACGCTTTGGCACACTNCTATCA ++ +!FF!!-F#!8!-F--#F--88-F!8#-8!-F!!FF!-8#F-F-!F!F8--F-----8-!FFF8!88F-8-#!F8!8!8F!-!8F-8!!!FF--F8FF8!FFF#!888F-888F!F-88FF-F-FF!!F!F!!F!!---F888FF#8-8F!8 +@machine1:HiMom:abcdeACXX:1:1101:1362:1000 1:N:0: +GGGTTAGTCCGCNGNCTGNTNCCTGCGNCACACGACTNATCATCCCCCGNTGTTTGGTTTNTTGTACGNANCATTCNGTCTCAATTCGGATTGGCGTCNTAGNAGAANTAACNNCGNCATCTATNATCTANGCCGTATNTTGGTTCTCCTG ++ +--8-!--FF-!8#!#-FF#F#F!--88#-8-F8F---#888F888-!--#!F-88-8F!!#F8888-!#8#888!F#88!F8FFF-8-88F8!!FF8!#F8-#--FF#8-88##!F#!-8!-F8#8!F8F#!F-88-!#-!--F-8F8F8! +@machine1:HiMom:abcdeACXX:1:1101:1398:1000 1:N:0: +CTCTCTTNTTTCTGCTGAAGACTGCGGTCCTTATGAATTNATTTACCTGTACCCAGTTGTGTTAGGTACATGNTTTGCANGAACAGACATTCGTCGCCCAGCTACCGTCACTCCGANAAGGTTAACCTGAGATCTGNANAGCANGCGNATC ++ +----88-#FF!-8F8--8-!F8!--8F8!F!88F!----#-8!F8FF8FF---88!F8-88-8-F-8888!-#F-F--8#!F---FF8F8FFF-88!8F----8-888-F8888FF#F-8!--8F8!-888F!!-!#F#--F-#8FF#88! +@machine1:HiMom:abcdeACXX:1:1101:1416:1000 1:N:0: +AACTTGGGTGCCCGCNNGCTCTCGAGGCTNGNACGTCATGCTTCGNTACGGTTACGCTNCTGGATCGGCACCTCAGTNTATNAATTGGAGCCCACNGTGNCGGATATGNTGNTGCGGATTNCATNGGTNTGGCGGCAGGGAGCCNCCCATT ++ +F-!F-8!-!F88-8!##!!---F!--!-!#-#F8-8-FF--8F8!#--FFF8-F-8!-#8!88-8F-!F8-F8-F-8#!-8#88-FF-8!FF888#!88#F8!8FFF8#!F#8FFF8FF8#8-8#F-8#--!F8!-FF!88!!-#!--FF! +@machine1:HiMom:abcdeACXX:1:1101:1434:1000 1:N:0: +TACTCNGTGGACTTGTATCCNGGACTTTCTCTCTGNTACTGGGTTNCGCCGAACTCCCCGTTNAGCCATCNCGGTGCTGGACCACANATCGCGTCNGACATGCGCACTAGNCGAACCCTATACTCTANTTCNCCTTCGCTTCGGCAGTTGT ++ +-888!#8FFF-F!-8!F!F-#!8-F888F8-8F!8#!FF!!8-!-#-8F!!8F8-F88!-F!#-!8-88!#-F8F88!F8-!F-F8#F!F!F!--#8-8-!F8!8-F-F-#FF8F-F8!-!88-!8F#!!8#88-8!F!!8F8!-F88!FF +@machine1:HiMom:abcdeACXX:1:1101:1470:1000 1:N:0: +NATCTTTGGGATCATGAATTAAGGATTGTCCATGCGACAAGCNATGTACNACAGCGNACAGAATTGNTACGATGAACGTCGTAGTTGCGTTACCAAGGCACTAGNATTACCCTCTNGGCCTCGATTCGNCCACCCTCTTGGNGGTCCCGAG ++ +#---FF8F888-F8-8F-!8F88F88FFF-FFF-!8F!F-!!#-88F--#F8888-#F8F!FF8--#!-8F88-8FFF!F8-F!F8-FF!88--F-F888-8--#8F88--FF8F#88-8-F!-F8-F#F8-!8F!F--F8#-F8!8-8F8 +@machine1:HiMom:abcdeACXX:1:1101:1488:1000 1:N:0: +GGTCCTGTTTATGCGTTCGCTGANGNTGANATCACTGCCGGATGGCTTNATAGGTTGNGTNATCTTACTGCGGGGCACTCAAGTTCCGCCCAAGCANGATTGGATTAATNCAGAANNATGNCGGTNCCGCGNGCCNTGTTNAATTTCATCT ++ +--!F-!FF-F-8FF!!F!F!--8#8#FFF#F!!8!F88-!F8FF!-!-#-!8!F!--#!-#8-----!F8!!!F88F-F8F-8FF8!F!8---FF-#--F-FFF-8-8F#FF88-##88-#FF8F#F----#-FF#8!--#-F-F8FF88F +@machine1:HiMom:abcdeACXX:1:1102:1000:1000 1:N:0: +CTTTTCGAGCATCGTACCATAGNTGTACGTCGTGTANCCCTAAGTGGCGGACTCCCGCCTTNGGACGGGTGCCCGTTTACCCACTNAACCACACCTGAGTACCCCACGGCGCAGCTCTATTGCTGTCCTCTTCTGCNTGATNTATTTGGNA ++ +--FFFF-FF-8-!!--!88F--#8!88--8---!-F#!8F-F8F!!!8!88--FF--F-F-#8-8-!!88-!8F!8FF-F-F8F!#---8F88!!-8F-F--8F-88!-!8-F!88FF-!88FF-F88!F-F!!F-#-F88#!88-!-!#F +@machine1:HiMom:abcdeACXX:1:1102:1018:1000 1:N:0: +NGGAAANGGATAANCCAGACACCCAANGGATATGTAGCATTGTTATACCGATCCTTGCCGCTTTTTGGTAAGCAGAGGACCATACGGTAGGGNGTGACCATGCTTCAGTCCCGGTTATATGCACTGGGCAGACGGCTGTCNNCTTTCGTCA ++ +#F---F#-!-!--#F88F8FFF!8-8#F-8-F---F8!F-F!!!-8-F-F88FFF888F!!-!8F!!!F-F--F-8F-F!F88F8!F!F8-!#!FF88-8-8-!!F8!-!8!-!!-FF-----F8--!88-8-8F-F!--##F!F-F-!-F +@machine1:HiMom:abcdeACXX:1:1102:1036:1000 1:N:0: +CAGTGTTTGTTCGAATCCGCTCCCTTCTGCTGACGTGGGTNNNNGGNAACCGAAACGCTTTTCTCCCACNCCGGNGTCGTTCAACTCTANATGGGACAGCGCATGGTTCGTCTANGCNTGACTCGTGGCANACGTCCTACGACCGCTAAAT ++ +F-!8--!F-F-8!F8F888!!!F8!F-8F!!F-F-F!-!F####!!#-FF8!F-F!8FF--8F-8FF-!#!--F#FF-!8FFF---F!-#8-F!!8!--F!FF8-88FF8--88#F-#!!-FF!F---!F#8F--88!F-!--!8!8F8-8 +@machine1:HiMom:abcdeACXX:1:1102:1072:1000 1:N:0: +GCGCTTGTTCCGATTTGTNTGGCGCTGCGGCAGCCTGATCGGNGCGCCTTGGTNGAGAGGCGCACTTGCACTANCGNCGGGCTACCGCCANACGTTTTCTCTGCCGGNAGCCGTATCCGGTTGGATNTTCCGNCCATCCACGAACTTCATC ++ +F---F!!-!8!F8F8--F#8F-8888!!--F8!-88-F88FF#!88F-F-FF-#FF-F-FF!-F-!FF!8--F#-!#F8FF-F8!FFF!-#F!F8F8!8FFF8!-88#--8!FF8F-8!F8-!8-F#8-!--#FF8!!--!!FF8FFF8!- +@machine1:HiMom:abcdeACXX:1:1102:1090:1000 1:N:0: +GCCTACGCATCCGCCCNCACTGNATGGGTGAGCCNGNACTAAGCTGTAGTGCCTGATCCCTCCAGGAGCCCTTTANTGAATCGGAACGCTATGCGACTTGTGATAACGAAAATTTCAGAAGTTNATCGCCAGTGTGGTTCTTCCNAACATG ++ +!-F-88F88!!8!--8#---8!#F8F8-!F--8!#8#8-8F-8-!-F888FF8!8F88!-F-F8!8F---!F8!-#8F-F8!F--8F!!!8-F8F8FFF!!!---8!-8FF8F!-8-!FF!F-#-FFF88-8!!8!!8-8!F-!#FF!8!- +@machine1:HiMom:abcdeACXX:1:1102:1108:1000 1:N:0: +TTANGGGGAGTGCNAAGGNCTTANAGTTCACCGAGCCCATAGCCTCNTGTTGTTGCGNGGGGGGTTCCTGTGCTGCCNTTGCGCAGAGCCNGTTTATGCTGAGGTNGCGGAAGACCAGTCAGTNATTGATGGGGGTGGGAGAGGGAANTAG ++ +8!F#8-8!--FF-#8-!!#8F--#-F!F8-!!!8F!FF-88!-!8F#8-F-8!888F#FF!88!8-8!-!!FF!F8F#!-8-!!-F8-F-#!!!F-F8FF-FFF-#-!F--FF8-!-F!--F-#-FF!F!-F-8F8---888--8F-#8-8 +@machine1:HiMom:abcdeACXX:1:1102:1127:1000 1:N:0: +GCCNAACGATCTTNTTTGCTCNNCGTGNTGCTTGGTCTTCTTGTCTCTAACTANCGTGTAGTGAGAGTNTCTCTCTCGAGCGTNTCTGGATTGCNCGACGGACGAGGAATTAGTGCTCAGTGTATCGGACCNTTTTCTGGCCGCATGCAGC ++ +8!-#8-8!-F!-8#!8-!88-##8-FF#FFFFFF!!F-F-F-FF!F--8-8-8#!!!!!88-!F-F-!#8---88!FF8-FF-#-!8-!88-8!#!8--F-FF8FF88F!F8F8!!8!-F!88-!!-F8!F#!8---!-!F!--8--!F!8 +@machine1:HiMom:abcdeACXX:1:1102:1163:1000 1:N:0: +GATACGGTGTTATTCTTCTTGATTTGACTACGNGTCCGACAACNTATTCGTGGAAACACGGCCCAATAGCGCTNGCCCNACAGCTTTATAGTGTCANCAGTGATTACGTCGNTGTCAGGGTTTACAATGNAGNGCAAGCGTTTGGCGGCGA ++ +!-!888F-8!!8!8--88!888---!8FF88F#--!F8-!-F8#F88F!88!!F-8F8-8!--!-F!FF!8-F#F!!8#-!F88F-!-FF!8FFFF#F-88F8F!8!!8FF#!8-!F888F8F--FF8-#88#-!--F88F!-F-!--!F- +@machine1:HiMom:abcdeACXX:1:1102:1181:1000 1:N:0: +TAGCATCGTAAACGGGACTTCGCTAGTCCAGTCTCTTACTAGTCCGGNTNTGGACTANNGTTNTGTANACCCGACTCGGANTNCATTAGTCACNCAGACTNCTGTNGNCATCAANGACCCNACNCCTCCTTCCCAGATAACCGTTNGTTTC ++ +-F!!8F!F!F--!F-F--F!-!---8F!!F-FF-!F8F8F--F--8-#-#-8!F!!F##-88#-8F8#-!-8F--!-!!8#8#8-!F88-8--#-F--!-#!---#-#F-8FFF#8888F#8!#F-888!!!-FF-F!FFF!!!F#8!F88 +@machine1:HiMom:abcdeACXX:1:1102:1199:1000 1:N:0: +CTAGCTGTTGCGGCGTTCACGGTGTCGTGGNCTTGGACCACGCCATCCCTCNAGNNCCTATAGTGANCTCAAATGGTGGTCAATAACTCAGGTTGCTGCGCTCCNTCNTGCAATCCCTGNAAACCACCGNTGGGCCCGGCAGTAGAGCTNN ++ +8F8!F-8F-8!!!8-!-8-!!!!F-!!8!-#8!!!-FFF888!--!-8F!8#F-##!!8F8-8!--#8!!-F-!88!!F!!8FF---!F88-!8--!!!-8F!8#88#!-F-8-F8F!!#--F8F8!8-#-8!F!!-F88F-8F-F!-F## +@machine1:HiMom:abcdeACXX:1:1102:1217:1000 1:N:0: +GGANTCCCCGTTNCAGTTCCTCTNCGCCAACGACTATCAACAGCGCGTACATTGGGCTGTGCCCTTCAGTGGGTTANGGCTTCGTNCGAAGTTCGGTTATGTCGTTTGNCCTNCCCATGNACTAATTCTATCTCCCATGNTATTGCTCCCG ++ +8F-#F--8!!!F#!88FF-8F8F#-FF8F8-!-!-F!-F-8-FF8F-8F!--8---F-8!!FF!F!F8-F-F-!!8#-FF!F8F!#8!---!-F-8-!F!F-F!!!!!#F8!#8!-F!8#8F!-F-8--F!-8!!-F-!#F8F--F8!FF! +@machine1:HiMom:abcdeACXX:1:1102:1235:1000 1:N:0: +TCTCNCTATCGTTNAANTATCACCTAGTTGGTNGNGGTGAAGTTGGATCTTTCTCTTATACACGGCAGACGTGCCGCTGAGGANTTCGCCNAGTAAGCGATCTTGGTTGCTCCAGAGTTGCGTGANTCGCTTAAAANGCGCGGCTGTCACA ++ +F!-!#!FF-F8!8#88#!FFF8-F-F!FF-!F#!#!F!-F--8!8!-!FFF-8-FF!--8F-!--FF-F8F8-!-F-F8-F!8#!F!888#8!!-888!-!-!FF!-8!!!8F88-!!--F-!!F#!F!88-88-8#FFF--!F8-F-8-F +@machine1:HiMom:abcdeACXX:1:1102:1253:1000 1:N:0: +CCTTCACACGTGACNTNTATCATTCTGTTCTTGTATTTGGATTGCCCTCANCNATATNGGCATCCTAAGCCCGGTNTGGTANTATGCCTCTCCTCGATCCCGACANGGTAACGTCCAAGGGANGGTCAGCTNACGAGATGGAGTTCAGGTC ++ +F8!F!-F88F8-8!#-#F8F!-F!!8!F!!-!F!-8--8FF-!8F-F!-8#!#--FF#8FFF-F--F8!-FFF-8#!8-FF#FF!F-8--!888!----!F8F88#F!8F8-!!!-8-F-!-#F-----!8#--8-!FF88FF-8F--!F! +@machine1:HiMom:abcdeACXX:1:1102:1271:1000 1:N:0: +GCCAATTCCCAAAGTGTCGCTCCTTTGCGCTTANTATGCGGTCCTCTACGTTACTNGGGCCATGGNGGGAACATNTTCNCAGTCTACATTGNNGGGNGTGCGGCTTTNCTNNCCTGTTCTNNGTCTCTANTGGTNGNCTCCATCCCGGCAC ++ +!F-F8FF!-!8-88-!--F-8F-F8F8!FF!!-#FF!F88F8-8--FF8--!8FF#!!8FFFFFF#8F8-88F8#!8!#--F8!!F!-F-8##!8-#8-8F-8!!-!#F8##-F-!!-8F##--F-!-F#!FF8#-#8!F--888-8F-FF +@machine1:HiMom:abcdeACXX:1:1102:1289:1000 1:N:0: +GCGTCTCAACATATNATTTATTCATATATGANTTAACNCAATCAGGAAACACCGGGACTTATCCGTNGGGTGCTNNTGTCCTCGTCTTGGTGCGCTCATNCTCTTTCCAGGTTTTAACGAGCGGACTCGATCCACTCTACATGGTACTTTT ++ +!-!8!!8FF----8#F-F8FFF8FFFF888-#!8F8-#!88!FF-888---8!8----888-!F8-#!-F!!8F##F8!-8!8F8F8-8-8F-8F!-8F#F8-!!----!-8FF!8FF!-FFF88-!-F-F-!8!-F8F!8F!-!-88!FF +@machine1:HiMom:abcdeACXX:1:1102:1307:1000 1:N:0: +ATCCGCATTTAGATCACTTTTCCNTCCCCATGCGATCATTGATGCCTCNGAAGTTACTGCCAAGTACCGCGNNCTCTGTCTTCCTTGGGGTTATTGGATGGGCTCCCCTGAAGGACATTTAAACACAGGATGAGCGATCCCTTCTNGTCAG ++ +-!!!88-8-!888F8F!!!8!-F#------8!!-F8---!8-----!!#8-FFFF8-!8-88F!8-8-!-F##F!-F8!8!FF-88!888FF-F8-FF8F!8F-FF-!8FF-8-8-F-88--F88--F----8FF8F8!8F8-!8#-88F8 +@machine1:HiMom:abcdeACXX:1:1102:1344:1000 1:N:0: +CTAGTGCAGGNNTGCAATCGTTGTGTCANGTGTTCTCGGAGAGAGATTCCGGNTCTTAGTTTTATNGGGTTGGTCTACNGCGNGTTNTCGTTTTTTAAGATTAGGCNCCGAATGCNCGAAGNAAAATGATGTCTGGCATTGTCTTCTNCGN ++ +!--!F8!88-##F---F-F!!!!88!-F#!!FFF--F-!FFFF--F-F!!!-#8!F-F-!!8!F!#!8F8!8-8F-F-#--F#8-8#!!-!-!FF-8---8-F8--#8!88--!F#!-F8F#F88FFFFFF!-!8!F-!F!8-!-!!#-F# +@machine1:HiMom:abcdeACXX:1:1102:1362:1000 1:N:0: +AGGGNCACTTTCGATTGATGNAATTCCATCCTATATCGATATTATTGTGTCCGCCTCAACTGNTGTCGCAGAATGCGCAATGACNCCACCNATGCAAGCTAGACGCGTGCGTCTTCGTGAGGTNAACTTACGATCGCTGGCCATATTGAAA ++ +8--F#8F88-FFF-8!!8FF#-FF-!-88FF-8FFFF!-FF--8F!F!--!F8-8FF-F-8!#8!8F!88FFFF!F-F-F8!F!#-8-8-#--8!-F88F-FF88F!FF!8!-!!!8F8F8-F#8F-F8F--FF!888-88!-!F-F8-F8 +@machine1:HiMom:abcdeACXX:1:1102:1380:1000 1:N:0: +ACTGAGTGGTATCGGACACCGANGCGTTAGNGGGTACGGCNGTGTTTNTGACCAAAGTTTCATCTCATCAGACATCCGTTTGGGCTGCNGCTTTGGCGCCATNGCATAGTGTCGGATCGACGTGTCACCCCCAATGCCTTGGTATTCGNTG ++ +8F8!F8!8!F-8F8--!-8!-8#8!-88--#F-8-8!-!8#8-F!F!#888!8F8FFF8F!8-F!8F8!F--FFF88!!FF88-F8!8#F!F8!8-!F8-8F#!-888F-F88-F8!FFF-F-!88-F-F8-F8-!88FF8-F-!F88#!- +@machine1:HiMom:abcdeACXX:1:1102:1398:1000 1:N:0: +NTCANAGGGCTTCGGCGAGCCNGTGNNCCATTTTCTGGGTAATCTCGATAGCGACCCGTNCGAGANATTTTATGATTGCGTTCGAAACTTAGTTATGGTGCANAGGCTNAATGGGTCCTGACTGAGTTTAAANGCGTTCACNCCCTTAGTC ++ +#-F8#F-!!-!-!F-!!88!-#-8F##F8-F8-F-888F-8-!-!!88F---8-F!F!!#F-8F-#---8-F8!8--8!FF!8!FFFFFFFF-!F-88!F-F#FFF88#8-8F--!-!F!-8FF8---8---#!F8FF!8F#F--88F!!8 +@machine1:HiMom:abcdeACXX:1:1102:1416:1000 1:N:0: +TGACTACTTAGTAACGGNGNCCGTGGCCGCTACTGCGCCGAGGTTTTTATGTTTGNCAACTGGAAGGAGGCAATAAACTAAGANCGATTGGCCCGNTAGGCNNCGCGTCGGAACAGTTTCTCGCAATCAACNCGTCGGCCNATTCAAGCTC ++ +!--88--FF-!!F-F-!#!#-88F-!-8F--8!-!8F!----FFF8!8F8FF!!-#FFF!-!88F-!FFFF8F!F-88!F8!-#-F8!8!8-F8-#!F!8F##!8-F!-FF-FFF!F-FF-F8!-F8FF8F#-8-F8--F#8F8!FF8!F- +@machine1:HiMom:abcdeACXX:1:1102:1434:1000 1:N:0: +CGGGGACAGTGTCATTATCGCCNCCGNGCAGGNTTAAGNCNTNCCGGNGGGGGCAGTGCTATTCCGATGTCCCCGNAATAGTCNTGGGTCAGTACCCATGCCCCTTATANAGCNATATNGTAGNCAGCGGCTTGCGGCTCAGCCCATTTTA ++ +-8-8---F!8!-8-!!FF8!!-#8!-#8F-F8#F--8F#-#8#FF8F#-8FFF8-!8-!-8FF!-!-88F88!-!#8F8F-FF#!!-F888-F-!-888!FF!8FF8F-#88!#888!#8FF8#!888!-88!!8--8!!-8-FF-88!8F +@machine1:HiMom:abcdeACXX:1:1102:1470:1000 1:N:0: +CAGACCGCGGCTCTGGATCACCTCCGACGGGTAGTGACANCTACCTNAATCCGTCCAAGCAATGTGCAGTTCTTAATGACTTGGCTCGAGTAGTCCTGACCAANGAACGGACGTTCTTCGANGATAGGTGGGAGNTGGCTTCACGCTTTAC ++ +8FF8-FFF!F-8--F-888-!!-!-8--8FFFF!!F8FF#!!F!!8#F8!8F8-8-8-F!--8-F!8----!F----8-8-F!!-F!F-!F-!!F-F!FFFFF#F--F----!!F-!!F--#88!F!F!8-F--#-F8-F-!-!!-!!!-F +@machine1:HiMom:abcdeACXX:1:1102:1488:1000 1:N:0: +CGCTGTGCGTAACTTCCATGAATATCGAGGTGGATCTCNGTAGTGTTTGNACNATAGGTACAAACGTCCAACATGTCACGTCGAGAACGCCCCGATGTGCGCGAGAAGTNATGAGCGTATGCAGGGCGTCAATTGCCCTTGAGAAGGTGGG ++ +FF--8F88!!-8-F8!-FF!88F-!F8F!F!!F--F88#!88-F-F--F#8-#8-8-8-8!F-88!8!!FF88!FF!-8FFF--8-8F8-FF8--8FFFFF-FFF8888#F8!F!888-F!--!88-8!---FFF-!!F!FF--8F88-!! diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/NN.2.fastq b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/NN.2.fastq new file mode 100644 index 000000000..e559f468e --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/NN.2.fastq @@ -0,0 +1,184 @@ +@machine1:HiMom:abcdeACXX:1:1101:1000:1000 2:N:0: +CCTGAAGAGNCNCANCNCCANNGGATGANAGTGACCACGGGATGCNAGTGCCCACGATGCGTAGGACGGGGAGCCATGATCGTCCGGGTTTGGCGTNCTATCGTGATAGGAGACGGTGCCCAGTGATGCCNCCGCGCACTGNTAACCCAGT ++ +F-!F8--8F#F#88#-#-FF##F-8!-8#88-F-F-F8F-F-F8F#-8!--8F8-!F!8F!--8-8!FFFFF8F!FFF-F-8-FFFF!8--88!8-#88F!88-F-F-F-FFF8--8--!!-FFF-F!!!#FF8-FFF!--#FF-F!-F-! +@machine1:HiMom:abcdeACXX:1:1101:1018:1000 2:N:0: +CCTCGNTAGGATCATCCTCGCGTGCCATCGCNGATACTNGCTTTATAACTTTTTAATACCACCACTTAAAGCNTTAGNTNTGCACAAGGTCGTACTAAAGGACCCGCTAGCGCGTGATCTGTGGTCCCACAGAGTACNCCGACTACTNTTA ++ +FF!8F#F88F-!F88--FF----8-F88FF8#!88-!F#-FF-8FF--88!F!FF8FF!8-F--8-!88888#!-8!#F#88F888-!--F--888F-8F-FF8F8---88!F!-FF!-!--FF--F88!-!-!FF!#!88F-88F-#88F +@machine1:HiMom:abcdeACXX:1:1101:1072:1000 2:N:0: +NCGGNCTGGTACCTATCGCGACGTCCACATTGTTGTATTCNGTTNCACAACCGTCTAGCCTTCTNTACTACCGCTAAGCTTAAANCCAACTGGACAGTGGGACACGGCTNCTCNGTCACAAACACCNACACAGCCTGTGCNNCACCTCAAG ++ +#FF!#F-8--8!-8FF-!-F--8!FF88-!-8-!-8-!!8#F8!#F--8-!8!--F88-F!F!!#88!8-F!----8888!-8-#88F-FFFF8!FF!!8F-8F8FF--#-F!#!!-8-88888--#FF8-FF---!!8-##-88!-F8-- +@machine1:HiMom:abcdeACXX:1:1101:1090:1000 2:N:0: +AGAGTGGGGAGAAGCGGTGGTGTGTTTAGATGTCGAANCATCGCCAGGTATTCGCGTGGTTTGTGGGCGCNCACNCTCATGAGTCACAAACTNCTTACATATCTTCGGGTTTCCAGTGGNTTCGGNCGCATCGTCCCCNNGGCATTGTAGC ++ +F!8!8!-!888888-8--FFF!-F!88FF8F-!F-88#!8-8F-F888FF8!88!--88FF!-8!-F!8-#-F!#!F-F!8F--FFF8-F8!#-!!F--F-!8!!-!-8F-8--8!-!!#FF!--#8!888F-!F8!-##F-!--!-888F +@machine1:HiMom:abcdeACXX:1:1101:1108:1000 2:N:0: +TGTGTGNACTATCAATCGACCAGTACTTAGTTCAGCACCGCCCTACTCGGCACTGCTAGCGGGTCGACCTGGATAGCCGTAGCGCGACNAGCGATTGTCTTGAGTGCTCGCCAGATCCTTCTGTCCTGTATTCATACANAGTGGGAAAGGG ++ +88!F8F#--!-8!FF8F!FF--FF-!!!--!F8F-!-!8F--!88FF!F-F---88-88-!-!!FF8!!-FF8!----!FF--888F!#F!88-8!-FF!F88FF8--8!-!8---!-888-F!8-8-F8-!88-FFF#-8-!!--F-88- +@machine1:HiMom:abcdeACXX:1:1101:1127:1000 2:N:0: +GCTTGCCATTTNCCGGACTCTATCCGTGCTCGTAGCACACNTATCGGCACGCCTTCNATACACTCTGACGACNGGCCCCTATGGAATGANTNGTCATCTACACCCTACTCATGAGATTTTAACGGGACAGTAGGCTACATCGGGTCAAACG ++ +F!888-FF!!!#--!F-F!F!88-F8!!!!-!---!8!F8#-8F!F-!FF!F-8-8#88F8-FFFFF-!--!#8F!F!-8F!F-F88F8#8#F88888--8-88!!F-8FF8-F!F!FFF-F-F888--8FFFFF--88-8-8--!FFF-- +@machine1:HiMom:abcdeACXX:1:1101:1163:1000 2:N:0: +GGNGCGCNCTCCGCACGCCANTAGCANCTTGNGTAGGCCCTTNTTTCCAGTTTCTGGTAGGTCTCGAGGCGTATCGTTTNCGGCGTCTTTCCACTGAAAGGGGGTCTTAGGATGGTATCTGGTNGCGNACGTGAGTGTATCGCACGTACCC ++ +F8#!8-!#8!8-8!88-!!-#8-!8F#8!!!#F!F--!!---#-!---8-!-FF!8!!F!8-8!!!F!--F!888!F--#F8F8-F8!F!-!8F8!-F--8!F!F8FFF!F-!!FF-FF88F8#---#8--FF-!!F!-F8!F888-FF!! +@machine1:HiMom:abcdeACXX:1:1101:1181:1000 2:N:0: +CCAGNNATTNGTACATACATTCACTCANGATCCGNCGATACGGTACCNTGTCTATTGANNAGTCACCGTCGGTCGACACCGTAGACCTGGTACGTNACTCTGTATNNCATAGTTTAGTNAGGCGTTGNCGGANGGATTGGCTNGCNATTCA ++ +!FF!##F--#!-F8--F!-!---!F-F#--8-F8#F-8!-8!8!F8F#!-F--8-F--##FFF-8F!!!FF!-8-FF-8!F8-!-88-8FF8--F#8-!8--!-F##FF!-888F--8#F8F-!!!-#F!-F#---!!FF-F#!8#88!-8 +@machine1:HiMom:abcdeACXX:1:1101:1199:1000 2:N:0: +TTTGAAATAATTGGGGCNGAAAAGCTTGCAATGTGAACTAGGTATGCATGNCANACGNGCCGTGCANNTNNTTTCCGAGATTGATGCACTGCGAATTAATGACTAGGGACTGACNNCGCCCCGCGTCCGGTCCTGTTTGGGAGGTAATTTA ++ +!F-FF---8-!F88F8F#--F8-F-8F-88-8!-F-88F-!FF8!F-8!8#!-#F!F#8--F----##-##!-!8-8--8-F-F-!!F8!8-F-F8F--8F-F8-F---F!8FF##88-F---!-8!!-!888-!!F8!8F-8!--8!!F8 +@machine1:HiMom:abcdeACXX:1:1101:1217:1000 2:N:0: +CCCTCCTCTCAATTATTGCTCTCATTCTCCNATTCGANNTTACGTTCTAGACGGTCTGNCAACCCGATTNCGTAANAATTGCGGGATCTTCTAATCATTAGTCCNGAGNGGCGTTCCGNTGCTCCGCANACAGTCGGATCCNNNAGTTGCC ++ +8!F---!8-8F8FF-!-FF!-FF8!!!!!F#-FF8F-##-!8!88!F!88F-!!8!!!#F8--FF!FF-#-88--#--F!F--FF8-!!F8!8F-!--FFF8FF#-8-#!-!F8F!-8#!--F8!FF8#8!8F-!8FF8--###F-!F--- +@machine1:HiMom:abcdeACXX:1:1101:1235:1000 2:N:0: +GGTACGATTACCANCCNTAGTTTGTTCCGAGNCNACCCGAGNCTCCGCGNACCGGGCTAGGTTATTTGCTTACTATTATAGGACTGGGGCGTTGGGGAGTTNCCAANCTAAAANTGTGCNCAGTGCNTATCTACTCACTAAGTTGCTCCGT ++ +-!!8!--8--F!-#!8#-888-!F!8-F!8-#!#F---88!#!8-!F88#F-FF-!F!-8!!8FF!!8-!-----8FFFF88F8F!!F!-8F!-!!---F8#8--8#FF---8#!8888#8F!-!F#8--!8-8-8-FF-88-8-F--F8F +@machine1:HiMom:abcdeACXX:1:1101:1253:1000 2:N:0: +TTCGATGNGTAACGTGCTAGCTAACAGNCTCANGGTCCCCGCCTTTCCCTTTAGNCGTCNTTCTCCCCCGTCCTAAATTGCGCTTGGATNGCGGGTTNGGTNTCACGGCTACTCATTCTACAATGACTNGNTATGGGGCATTCCATAAGGN ++ +F-8!--!#!8F8!F!!F!FFF-8-88!#!-!F#-F!8!88!-88--8!-8!-8!#F-F!#!!!F!F8!88F8-F8F8F8-F---88!F-#!FF8-!F#F8-#--8!F!--8-F8-!-8--8--F8F8!#!#!8!!8!88F-F8!F88-F!# +@machine1:HiMom:abcdeACXX:1:1101:1289:1000 2:N:0: +CATTTTCGTNNTNACAANGCTCTAGTNGGGCANCAGGCGGGGGGACTAACTTAGGAACCCGNNGAATTCAGGACTATCTGCGTACGNACAGNGGTTGCAGTGACGGGAGAAGNCGCNATCGCTNTGTTAGTGTTCCTGCNTACAGGGCACG ++ +--8!!!!-8##8#8!F8#!-F!!F-F#-F!-F#--FF!888-8!--!--88-FF!-8!!8F##--F!--FF-F8-F8!!8!8!--F#F---#-!-F--FF88F88F!8!88-#!8!#8F8!8-#!8--8-!-!-!-!8!#--!--!-FFF- +@machine1:HiMom:abcdeACXX:1:1101:1307:1000 2:N:0: +AATTGNCTTTGAGATAGAGGGCCCCTACGGTTGTCTANTACTCTGTGCCAGAAGCCCAGTCGGNCGGGCAACTTTCCGGCTCCGGCTTTTGNNCGCGATGCANATTTNGTTTGAGGCGCTGGTTCCCTCACTTCAGATTGCCNATTCATNC ++ +8F!-F#F-!88F8-F8!8F!!!-!!8-F--F8-888F#8-8-!8F-!!-88-8!FF8FF8!88#8-88!-F!F88F-F--8--F88!8FF!##--8F--F!F#8!!8#--!-8FF88!-!-!-F!F!F!--!-!---FF8-8#8-F88F#! +@machine1:HiMom:abcdeACXX:1:1101:1325:1000 2:N:0: +CCAGAACATCCCCTGGAGCCTGGTCTACTNGGGGACAGGGTGTGCGTNGCACNGGGNCGGTTCGATGGGGGAGNGGCGGGACTCCTTCGCAGCAAAAGAACCNTAATTTTTACCTTCCTTTTGTGAAGTGCTAGCTANGTTCGGGNTNTCG ++ +8---F-F-F-!8!!-!-8-F888!F8-!F#F-!-8!8-!-F8---F!#-F8F#FF8#88!-!!FF8F8-!F8!#8F-F8-88F!--F8!F--8F--F-F--!#F-F!!FF-FF8!8!!--F-!-!8F8F!!F-!-!8#FF8!8--#F#!!F +@machine1:HiMom:abcdeACXX:1:1101:1344:1000 2:N:0: +NCGAGAACGCCTTCGGTCGATCTACTCCNGATGCTTTAGGAATGCCATTNCGNTGCCTTNGCTATTACGTGCCGGCGGCCGTTTTCCAAGTGCTATTANCCTTAGCGGTCCCGTCTCATGTCACGGAGAAGAGCTGTTACTATGACGGTGG ++ +#FF-8F--8!8--F-FF8!8!-!88F!8#!8F-8!---F-F8-!!FF--#!F#8-!!!-#-FFF8-FFF8-8!-88!!8!F8-FF!88F!8!8---8F#-!FF88F-FF8!-F--8-FF!888!!!-8-F!FF!!88-8-F8F8-8FF!8- +@machine1:HiMom:abcdeACXX:1:1101:1362:1000 2:N:0: +CGCTATTGTAACGATCGTATTTTACTTNNTCTNTCGCACAGGGTATAGNCCGGGAGGAGGNTACGGCCTCNAGCCGTGCGCGCAGGNNGGGCGTAATCCTTATGTCAAAATTGCTNCACTACNACGTCTAGCAAGCATCAGGAGGAANAGT ++ +F!-F8F!F!8FF-FF8888!!-8-8F!##!-!#-!8F-88!-!!--8!#F--!F-FFF--#!8--!---8#8FF----8-F-F-!-##!F8F!88-F-8-8-!F-8F8F-F!!8-#!FF8F8#88F-F8F8!--F!F88F8FFF-8-#--! +@machine1:HiMom:abcdeACXX:1:1101:1398:1000 2:N:0: +CGTCCTGTACGTGTCGTTAAACTGTCNCNGCNTTGCGTANGGTGCCGTGCACGGTATAGCACGTTGGCATGGGCGAGCACTCACAACACACTGCNGGGNGGGATTGGCTGAAANGGAGCGTCGTTAAGGGCGCTAATGACCATGTCNCAAA ++ +8F8---!-F!F8F-F88-F--F!8!!#!#88#!!F--88#-F8F8---888-!88FF-!F-8-F--!!-!FF8F888--88!--8F88F-8F!8#-8F#!FF8-!F--!88--#!88F--F!888F88!8F8!FF-!8F8-8!F8!#F8FF +@machine1:HiMom:abcdeACXX:1:1101:1416:1000 2:N:0: +TGGTCCTCTGGTCAGCAGTTCTAAGTGCCGTCTATGGNTGGGTNCACCANCGCTANGTNATAGGTCCCTAGGTCGGGCGTGCGACTCACCGCCGGAAGGGGTGGCCGGGNTATTTCTTCCAGGCAAGCCANCTAATGGTAAATCTGTCGCA ++ +-8F8F-!-!--F!F8-F-!F888FF-F--F8!--888#888!!#-F-!-#F-8!F#!!#----!8-!!88F8!!F8-888!FF8!!88!8FF8!---F!F88!8-8F88#-F----F--8F-!FFF!F8-#-!-F!F88--8--!-8-F8- +@machine1:HiMom:abcdeACXX:1:1101:1434:1000 2:N:0: +TTTGTTTCAGGGCCTTTGCCGTNCGCANTATTGTGTCTCTTCCCAGCAGCTGTCCTTAATGATNTAGCAGATCGCCTGTGCATTANCGCACCTCNTCGTANAGGGGTGTTCCAACGCATACANCTGCNTGGNCGTNNCAATGAATCAGATT ++ +--!!F!8!FF-!-!88!88!-!#8-FF#F888F!!F!8--8F-!FF8-!F-8FF!FF8F8!88#8--!888!-F!FF8F8F-F-F#!F!88F-F#8!!F8#-!8!---88!--88F-F-88F#8888#-F!#FF!##!F8-!-8F8F-8F- +@machine1:HiMom:abcdeACXX:1:1101:1470:1000 2:N:0: +GGGAATTCCGGTTTTTGGCGAAGTCTCGATAACTTCCGCGCGGCACCTAACTTGCCAGCTGTGGTTCGCGTCGTGANTTAATGTTGGGNTCTCGCNCGACATAAAANTGTAAAGGGAGGCCTTGGAGGCCCNGGTGTATGCTNCCAGCTGG ++ +--!-8F-88F-F---!8!F--8FF!8F--!---!-888--8F-F--!8FF!8-FF!8-!8-!----8-!8-88FFF#8!-8!-!-F!8#-8-!!-#8F888F8FF8#--!888!8F8!F888!!-F8-!-!#F-888F!8!-#F!F8F8!F +@machine1:HiMom:abcdeACXX:1:1101:1488:1000 2:N:0: +GGGGGTTAACCTCGTGTNCGTANGACATATTACACGCTAGGACCGCAGGTGTGGAGCGNTNTCTNCGCCGAAGGCTTTAGGTGNCNAATCTAAATCTGTTGCTGATCTTANGCGCATNGTATNCCGTGTATCTGGAGTAACNCATAGGTCT ++ +-8--8F!F8-F-F!F-8#F--F#!8F--FFFF!-!!F!F-8F!8!FFF!8--8!F-!F#8#-!8#!8F-FF8----F-8--!F#!#888-8-8FF!8!88---888!-F8#!FF!-!#F!-8#-!F!8F88---!8!8-8F#-8FF-FF!8 +@machine1:HiMom:abcdeACXX:1:1102:1000:1000 2:N:0: +GGNGTTCTGTGNCTCTTGAGCAGTGCAGCCCGCGATGCGCCGCGCATTCATTCCATATCGGTTTNGNATANCGTTACGCCTGCGTCCGCGGCNCCTGATGTCCTCGGNAGATTACGTGGTAGCAACATCATNTGCATTTGTCGCGGATTTT ++ +--#!!F----8#88FFF-F--8!---FFF-!888--!8!F-FF8F8FF888!-F-F-FF!!FFF#8#8--#-F-FF8F-F!F!-8F-F-!-8#-8F88-8-F8!F-F#FFF!-FF--!8-F!F-8-F8FF-#!F!FF-FF88FF-F-!F88 +@machine1:HiMom:abcdeACXX:1:1102:1018:1000 2:N:0: +TTTCACCAGGCCTCCTCGTAAGTAGATCTTATTTGGATCCAGGTAGCATCGGGGGAGCCGACATTNGTCCNGTCTCAGCGTCGTCCACCTACTCTGACGNGTACCAGAGTGCTCCCGGTACCTCAGTGCCAAGTCGGATTAGCTTGCCAGT ++ +88!!8-8F-F-F-8-!!-!F88F-F-8!FF-8F!8!F!8FF-FF88-F8!F!!8-F!F8FF8FFF#!8!F#8888!-8-!!F-F!F-F8!-!88!--F-#!F88!F!-!F!8-8F!!-!F!--F--F8-!8888F!!8F88!!----!888 +@machine1:HiMom:abcdeACXX:1:1102:1036:1000 2:N:0: +TTCCTCGNACGTCTTTGNAGANTTTCGCCCAAGGCTTGTCCNTGCAAGACGTCCTGTCGTATAAACNGCCACGGGCGGCTAGGACTTGGANACGGACCTNATAGTTCCTGTGCCACTTNTCGNGTTTTCGTCTTGTTGNTGCGANAGGGGN ++ +F-!--F-#-8-F!-F--#-!-#88888F-FFF-F!8F!--!#-!-88-F!!F8!88-8-!8--F88#-F--F8FF!-F!!8F8FF8FF-F#--F-F8-F#F-F!F!!FF8!!F!88!F#!-!#-!--F8--!-8!8-8#F88-F#-8-F-# +@machine1:HiMom:abcdeACXX:1:1102:1072:1000 2:N:0: +ANGAGGCNCCGCCCCNNTTNCTCGTNGCCCTCCCAACCGTGCGACTGGNNGCGCTGGACATCGTCGCAACTTACGGCGTGTGCCCTGAAGGTGACTACACCGNTGAAAGGNCGCCTCGCCGTCCATGCCACAAGGTGGACGNTCATCGNCT ++ +8#--8F-#F8!F!F8##88#-!F-8#F!-F---FF-F8-!8-8-8F8!##--F-F-8FF-FFFF--8--!8--F--!FF!!-!888FFFF!!!-!--F-8!-#--8FF!-#FF-!8F!-F-!-!8-888FFFF-8!--8!!#-F-8F!#!8 +@machine1:HiMom:abcdeACXX:1:1102:1090:1000 2:N:0: +TGAGNAGNCGTTTTTTGNCCGCTACCTTGNGGTGTGCGTGCCTAGGCACTNAATCTCCCGCTGTTGTAGGTCTATGTATTCNNCGTGATGCCGCNGCTGATGCTGTNTTCTGCGTCGCNNGCCTGCNCCGTTGCATATCGTGGCGGTAACA ++ +!FFF#F!#-F8F-8-!8#8F!8F--!-!8#!!--8F-F!F!-F8!--F8!#F-!8!F-8!FF-!F-8--!8!!FF!!F!-8##!---8!8!--F#!!F--FF--8-#F!F--FF!F8-##-8F---#-88!--F-FF8!FF88-!!F8-!F +@machine1:HiMom:abcdeACXX:1:1102:1108:1000 2:N:0: +TTTTCCAGTCNTTCTTGCAGGCCGGTGCATCGGCTTNACGCAATGNCCCCTCNACGTTGTGAGTGTCCCGATCAATTTGNGCNNAAGTACCAAAGGTGCCTGTCTGTAGTTGAACATTACGTGGCGTATGGNGTAAGTTTCTATGCACGCG ++ +8FF-8F8-88#F8--8F!F--8888F-8F!!--!8-#8-8-8--8#8-8F!F#8!F-F-8!--!8-!!8!88!-F!!8-#--##F--8-!-8-F!FFFF88!8-8FFF-!F8FF8FF-F!--F88-!-!!8#-F88!F8F!8-F-8-F--- +@machine1:HiMom:abcdeACXX:1:1102:1127:1000 2:N:0: +CGCCGCTATTCCGGACANATNGTGTGACGCTTTCCGTCTCCCGTCGTCTCGATTTGGCGCCNATCNTCCGTCAGCCTAGAGNANTAACGAANCTGGATGCTGCNCATTGGANATGACTACCTGCTACTTGGNACGATTCTGCACGTCGTCT ++ +!88F8FFF!8888!-8-#F8#-8!!F-!FFF!888--8FF-F-F--8-!FF8-F888-F!8#F--#!88!!-F-FF!F-8-#-#!--FFF-#8-8-8-!-!-!#88F!!8F#F!8FFF8-F---FF!-888#F8FF8------88--8F!- +@machine1:HiMom:abcdeACXX:1:1102:1163:1000 2:N:0: +CCTGCTCCTCGGCCGACCTGNCCCTAATGCAGTTGCTCCGGANCTGCCAACGAAAACCTTACTCNTCTANCTCGTANACTACGGCACTGAAGCANTCNGCCCNTTTGTTCNCGTCTAACCACTCTTTCTTCGCGCGATNTAAGGCCTNCTC ++ +F!-!-F88FF-!F-88F!-!#-8!8-F!88--8F!!FF--8F#-FF88FF---F8F8!88F8!-#F!!8#88!-FF#-!FF8!F-F!88F----#!-#-!F-#8!--!!8#88FFF88F8-8!!-!F888!!FF!8F8#8-F!!!-8#F!- +@machine1:HiMom:abcdeACXX:1:1102:1181:1000 2:N:0: +GACTNAGCGATAACGTGGTTCTACGGCNCNGTATCNCTTACGTGGGNTTCTCAGNCGTGCGAGCCCGTGGCCCTGTGCCTCTNTCCNTCGCTGTTGGGTCCCTCACTATGGTTCGCGTTCTGCAGAGTGTGNGAGTTAACTCNCNGACGTG ++ +!8-8#-!!!F!888!!8F!!F!F!-FF#F#--FF!#!-888-8!8F#-FF!---#---F8-8!-88FFF8-F-8!F!!88!!#FF!#8!!-8FFF-F--F!!8--8FF!!---F888!-!F!8-F8!88!8#F-F8-8-F--#!#8888!F +@machine1:HiMom:abcdeACXX:1:1102:1199:1000 2:N:0: +TGTGATCTCACAGTNTCGATTANTTCGGTGGCTNATAGATATCGCGTGGNGTCCGGGTCGCCGCATCGGNCTTCAGCNAAGTTNGTCGTTTTNGCGAATAGCAACGCGGTGGGAANAACGTTGNGNGATGGTTGGCGGTNTTTTAGTGCTT ++ +!8----8F-8F---#--8F-8-#8!8-!8!F-F#8-F!F!FF--F-F88#!FFF-8F!-8F--!-88!!#88-!888#---!8#!!!!8F!8#F-!-FF-!-F---F8!-!-8F-#F8-F-!F#!#8F-8-8F-F!--!#FF88F8-F!FF +@machine1:HiMom:abcdeACXX:1:1102:1217:1000 2:N:0: +ATGCGTTTNGTGCATANAGGGGTCCAGTCTTCACTTGTTGACNANGCGAACCACANNTCGCCGTTTGGCANCGTCAGGTCTTGGGAGTTCGGTCGCGTCATGTTGCGNGTGACCAGGCCCCTCGACTGCCTACTTCGCTTATCGGGCGGTN ++ +FF888F88#---F-!8#F88!8!FF8F8F!8F8!FFF!!-FF#8#--!FF8--!8##!8F8!!F!-FF-8#F-8--8!8!8F8-F8FF-8!88!8-F!88-FF8FF8#8F!F-F8!---8!F-!8!!F8888F!FF8F8--FF!--F-!8# +@machine1:HiMom:abcdeACXX:1:1102:1235:1000 2:N:0: +TCATAATGGGACTNACGGGCTAAGTTCNGCGGCGTNACGGNCTAAATGGGGCACNCCCCGTCTACTCTTGCTCATATGCTTTAAANGGGGCGATTTCNGCTTGCGGGATGCGGACGTCCCATGTTTTCANGGGCCGCCCTAGTCCTNNGGT ++ +!-F-8F-F!!8F8#-8-F!!!-8--!-#FFF--88#8!!F#-8-FF-8!-!8F8#88F8!8-F----8F-FF!F8-!8-8F8-F-#!8-88-F!F8!#88!!8F8---!!8-FF-!888-F-F-8-8-F#8!!-!F!!8-8F8-8!##-8- +@machine1:HiMom:abcdeACXX:1:1102:1253:1000 2:N:0: +GGCGCCCTNCTGTCATCCGTATGTGNTCGCTTGATTTANCCGCCNATATGGTGGCTCATCTCGCTCGGGGACCATGCCTATTAAGNGGGNAGTCTGTGGTTNAGTGCTCTTGANCGATTCGCCTTCCCNNAAAAGGTCTGACGTGCCGCGA ++ +-!F--!FF#F-!!FF--8FF8F--F#F-FF!8F88FFF#-FF8-#-F88---!8F8-8-8F-!-FF8!-F88!FF8-!F-8F88!#--F#--!-888F-FF#-!8!88-!!88#8FF8-8!8F!!8!-##8FF8F!!-F!F!-8FF-!8!8 +@machine1:HiMom:abcdeACXX:1:1102:1271:1000 2:N:0: +GNGCCGTCTTTAATGTCNTNGNACCTTATAATTCCGGNGCACGGATAGNGCGACTGCCCGCCGCGNCTTTCCGAGCTTTTNTAGTCGGTGTCTGTACATCNGCCCGGCATCTTGCTTCCGACATCGTCNGGGGGCNAGTATTGCAGACATA ++ +8#!!8!8F-!!88-8-F#F#F#FF8!-F8FFF-FF8!#-FF!--8F-!#F8!88F8!-FFFF88F#F!FF--F-F-FF-F#!8-8!F8!8--8FFFF-F-#F!8FF!88!!-8!-8!!F88F8!F-8!#!8!F88#--F8FF!8FF-F88F +@machine1:HiMom:abcdeACXX:1:1102:1289:1000 2:N:0: +TTAGCAGCACANCACGGCTTGTTGCGACTGGTCGTCTNACCGTTCTAGTANGANGCCGGTGTCTAGGCCCCAANGTGTCGCAACGGACCCCGGTCCCGCGNCCNCACCGANCATGNTACTCGNATCTNGATAAGGTCCAAATTGCTTCTNG ++ +!88!--8--!F#-8!-!----8F-F8F8!8!!8FF-8#88!-88-8F!!F#F-#8!FF88!F-!-!88!!8--#!8-F8F!-FF-F-8FF-!-F8FF88!#--#!-8!-F#--8!#F8FF88#-8!F#F-!-8F!88F88F!--!8FF!#! +@machine1:HiMom:abcdeACXX:1:1102:1307:1000 2:N:0: +CGAGGATAGTANATCTTTTCANGNTGCCTGGCAGTATCAGTCAAACTTGAACGGGTACGGGGAGAGGCTGTCCTGGGTGNAAGACCATTCTCCACNGCGAATGACTAGAGTTGCCCATGATGGANTATGNTNNGACGAANGTGCGTGCATN ++ +!-F-F8!8!--#--88F---F#!#F!FFF8!FF88-8F-F!----FFF!F8-FF--F-F-F!F!F8FF-F!F-F!!FFF#---88F8!-!F-!88#F-FF--8F-F-8F8FFF-FF8!8----8#!F88#!##!8FFF-#!!88!8F!F-# +@machine1:HiMom:abcdeACXX:1:1102:1344:1000 2:N:0: +CCCGTGCTNNTCTTACGNGTACGTNCNNTATAGTCACGNAGNGAGTAAACNCAAGTNCCGGCCGCCTCCAATATTCCTTTGATTTATCNAGGGNGACNGCATCNGTCAATGTCANCAACATANATCCTGTTAAGTNGGCTAGNGCACTCAA ++ +!8!-8!F-##8!8!FF8#!-FF!F#-##-8-F!F8--!#8!#!FFF8--8#-F8-!#-F!-F!F88!F!F-FF-88-F--88FF-8F-#--!F#!--#8-8F8#88F8FF!-F8#!-8F88-#8!F8F!88F88-#F!8!-!#F8-!88F8 +@machine1:HiMom:abcdeACXX:1:1102:1362:1000 2:N:0: +GACGTGCTGCTGCGTCCGTAGGNGCNCCTATACACAGGANCTGTGGGATGGTTCAAAACTGTCACNNCGNGGATCTCGGGCNGTGCCTCGGAGTCAGCCTCTTTNGATGGTGAGAGAGGTCTGGTANACGAGGTTTCTAATGTTGGTCATT ++ +-F-F8F-8-8--F!8!-8!F!8#8F#8---F-8FF8F8F#F8-8F!F-!--!8F8FF8F--FF-F##F8#FF88!FF!!--#FF88!!!F--8---!8888-!F#!-!F--!F8-F-F-!-!8--8#F--FF!F-F-!8-F8-F-!F--F! +@machine1:HiMom:abcdeACXX:1:1102:1380:1000 2:N:0: +TGAGGCCGGAGCCGCGCCTTNCATGGNCCGGTGATTATGAATGCCGCTGTTCCTTNTGNGTAACGGTGTGTAATTGACGCGCACACCCTGAGCNGGTATNGGCNATCNGGANACTCCAAGTAGACGCCGTTCCTCNGATCTANACGNGTAT ++ +F-F-88!-FF-!F!88-!!8#!88-F#!F--!F-!-FF8F8FF8!--8F-FFF!!#8!#8--F!FFFF!!!F888-8F-88F888F-!!--8-#-!F88#FFF#F!8#!-8#---!!8FF-F8FF-8-F!8----#F--F88#F!F#!88! +@machine1:HiMom:abcdeACXX:1:1102:1398:1000 2:N:0: +GCTCGCTTANCTAGAACTCCTTCCACAGTCCCCCCCGTGCCTCCACGCGNCCAAGCNTCCGGGGCGTTACATGCGCTCGCCNAGGNCTATATGCTCTCCCCGNCTTNTCTAAAGTAGTTTTCCGGGTCGAGTATTAATAAGAAGGTAAGTN ++ +!F-F-88!-#8F88F-!-F!FF--F-FF!8F-FF8!FFF!-!8-8!F!!#!--F8!#F-8-88!!F!--F8F-F-F8F88!#-8-#FF--F-!!-F-F!F-F#!8-#F8F8F8F!FF!-F--8F!!FF!-8!8-FFF!F-F8--8!-8--# +@machine1:HiMom:abcdeACXX:1:1102:1416:1000 2:N:0: +TCGGCACGACTACTAGTAGCACNCCGCCTGGGTCACNTAGCCTCAGTTGGCTCAAATTTGGCTGGAATGACTAATCATATTTTGTCCATACAATCGATCTTTGGGCCTCCCNCCCCATNANCCGCGGGGTACCTTGTGCCTCTCACTTGCC ++ +-8!FF8!!8F8F8F-!!F8-8F#FF88!8-!!!FF-#-F8FF8F-FF-F-8-!8FF88!8-88-88F!-F!F888888-!!F8F!!FFFFF---!FF!-!F88--8---!F#-!8FF!#F#!-8!--!FF-!!F88!8FF--!88F88F!! +@machine1:HiMom:abcdeACXX:1:1102:1434:1000 2:N:0: +CCCTATTGCACTTAGNGCGTGGAATCGCGGGATTNCGGCCCCCGNCAGTCGGCTATGATTCGANTCCATGCGTGCGTGTGTGCGTATCCCCACGTATAAGAGCGCGGACACTCCANCTGGGAACCAATCNCANTGACNTAGCCGACAATAT ++ +-8F-F8!F-F8-888#F8FF!!F8F!-8!8!8F-#8F!--8F!F#-8!F!8!-F8-!8F-FF-#-8--8!!88-----F-8--!!888!-F8!-88-----!8!88!8-8-!!-F#!--8!8-!!8--F#!-#F!--#F-F!-!-!F-F88 +@machine1:HiMom:abcdeACXX:1:1102:1470:1000 2:N:0: +AAGCAANGANGACACCGGTGTCAGTGTTTTGGNATCGCAGCTTTNGACCTGCTTCCTNAACTTNTCTGTTTCCGAAGTCACTTATTNTAAACGAGCTCTGGACTAGGCTCTGTACTCCCAATCTCGTNNTCTCGGGTCAANGAGCCTGGCC ++ +F8-888#!8#-8--F--!F--888!8F8!-F8#-F!!!--!F8-#--8--F-!8FFF#--F!-#!F-!!!F-8-FF8--F!-88!8#88-F-F-8F--!8!F!-8-F--!88FF!-8!--8-!88F!##-!8-!!FF8-F#8FF-!!!--- +@machine1:HiMom:abcdeACXX:1:1102:1488:1000 2:N:0: +TCCTGACGGATACTTGCATAGGACNCACTAGGTNTTGTCTATCTTTCAACGACAGGGANANTGTAAGGTGTTGAGTGTTCTCATGGCGTTATGGGCTCTTTCNCNATTGTAGAGNCGGTGCGCNAGGCTGATTGACCCCGCATTGGGAATC ++ +!-8F--!FF8888!F--8-88-88#888-8!-F#F!-8-F888!!F-F-F!F!F-8-F#F#!F-8--FF--!--FF-!F!!88F!8!8-8-!-!-!F8F888#F#F!!!---F8#-F-F-FFF#8--FF-88--F--888FFFF88-8F!F diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/NN.barcode_1.fastq b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/NN.barcode_1.fastq new file mode 100644 index 000000000..7ea2456b1 --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/NN.barcode_1.fastq @@ -0,0 +1,184 @@ +@machine1:HiMom:abcdeACXX:1:1101:1000:1000 :N:0: +GCCNAGTA ++ +FF!#F-!F +@machine1:HiMom:abcdeACXX:1:1101:1018:1000 :N:0: +CTTCGTGT ++ +FF-!F888 +@machine1:HiMom:abcdeACXX:1:1101:1072:1000 :N:0: +CTTCCTTG ++ +88!-8-!! +@machine1:HiMom:abcdeACXX:1:1101:1090:1000 :N:0: +TCTCACTC ++ +F!-F8F!- +@machine1:HiMom:abcdeACXX:1:1101:1108:1000 :N:0: +AGCCCCCT ++ +8F8---8! +@machine1:HiMom:abcdeACXX:1:1101:1127:1000 :N:0: +CACTTTTC ++ +FF88F!8F +@machine1:HiMom:abcdeACXX:1:1101:1163:1000 :N:0: +TGTCTATT ++ +F!F!F8F- +@machine1:HiMom:abcdeACXX:1:1101:1181:1000 :N:0: +TGTGTCAG ++ +-F8!!8F8 +@machine1:HiMom:abcdeACXX:1:1101:1199:1000 :N:0: +ATGTCNTT ++ +FF8FF#-8 +@machine1:HiMom:abcdeACXX:1:1101:1217:1000 :N:0: +GCGAGGCT ++ +F!F8-FF8 +@machine1:HiMom:abcdeACXX:1:1101:1235:1000 :N:0: +CCATCTGT ++ +8!8---F8 +@machine1:HiMom:abcdeACXX:1:1101:1253:1000 :N:0: +ATTGGTGA ++ +-F!-8-8- +@machine1:HiMom:abcdeACXX:1:1101:1289:1000 :N:0: +CCTGTCCG ++ +8FF88-8- +@machine1:HiMom:abcdeACXX:1:1101:1307:1000 :N:0: +TTTATTGC ++ +!!!8F!FF +@machine1:HiMom:abcdeACXX:1:1101:1325:1000 :N:0: +TGTCCTAG ++ +F-F-!8FF +@machine1:HiMom:abcdeACXX:1:1101:1344:1000 :N:0: +TTATCTGA ++ +-F8!FFF8 +@machine1:HiMom:abcdeACXX:1:1101:1362:1000 :N:0: +NAGGTNTG ++ +#-8!F#!- +@machine1:HiMom:abcdeACXX:1:1101:1398:1000 :N:0: +NCATNCTC ++ +#FFF#--8 +@machine1:HiMom:abcdeACXX:1:1101:1416:1000 :N:0: +TAGCGTTN ++ +-F88--8# +@machine1:HiMom:abcdeACXX:1:1101:1434:1000 :N:0: +AATTTGCG ++ +-F--8!!! +@machine1:HiMom:abcdeACXX:1:1101:1470:1000 :N:0: +GANCGAAC ++ +FF#--F88 +@machine1:HiMom:abcdeACXX:1:1101:1488:1000 :N:0: +CGTCNTGT ++ +FF8-#-!! +@machine1:HiMom:abcdeACXX:1:1102:1000:1000 :N:0: +AAAGCGAG ++ +F8-F--F! +@machine1:HiMom:abcdeACXX:1:1102:1018:1000 :N:0: +TCGTNTTG ++ +--F8#-8- +@machine1:HiMom:abcdeACXX:1:1102:1036:1000 :N:0: +NCATATCT ++ +#!FF-!!- +@machine1:HiMom:abcdeACXX:1:1102:1072:1000 :N:0: +CCCATGCC ++ +!!88-FFF +@machine1:HiMom:abcdeACXX:1:1102:1090:1000 :N:0: +TTGCCTTT ++ +!888!8F! +@machine1:HiMom:abcdeACXX:1:1102:1108:1000 :N:0: +CCCGNGCT ++ +!!F!#888 +@machine1:HiMom:abcdeACXX:1:1102:1127:1000 :N:0: +GTGGCAGA ++ +8F8-FF88 +@machine1:HiMom:abcdeACXX:1:1102:1163:1000 :N:0: +CCGCGCNC ++ +--8!--#8 +@machine1:HiMom:abcdeACXX:1:1102:1181:1000 :N:0: +CGCGTAGT ++ +-88F!88- +@machine1:HiMom:abcdeACXX:1:1102:1199:1000 :N:0: +TAACGGGT ++ +-8FF-!-8 +@machine1:HiMom:abcdeACXX:1:1102:1217:1000 :N:0: +CTATCTGN ++ +8-F!!FF# +@machine1:HiMom:abcdeACXX:1:1102:1235:1000 :N:0: +CCGGTGCN ++ +!888!!F# +@machine1:HiMom:abcdeACXX:1:1102:1253:1000 :N:0: +GANGCTGA ++ +-F#8!-!F +@machine1:HiMom:abcdeACXX:1:1102:1271:1000 :N:0: +CCCAAGAA ++ +F!88-88F +@machine1:HiMom:abcdeACXX:1:1102:1289:1000 :N:0: +CGCTGCAC ++ +8F-!-8F- +@machine1:HiMom:abcdeACXX:1:1102:1307:1000 :N:0: +TCGGTCTT ++ +-8-8!8F! +@machine1:HiMom:abcdeACXX:1:1102:1344:1000 :N:0: +CCAGTCAC ++ +!F--!!88 +@machine1:HiMom:abcdeACXX:1:1102:1362:1000 :N:0: +CAACCTAT ++ +8-8-!8F- +@machine1:HiMom:abcdeACXX:1:1102:1380:1000 :N:0: +GNGGTGTG ++ +F#888!-F +@machine1:HiMom:abcdeACXX:1:1102:1398:1000 :N:0: +GGTGTTGT ++ +-8!-8F!F +@machine1:HiMom:abcdeACXX:1:1102:1416:1000 :N:0: +TTAGCGTG ++ +!8F8F8FF +@machine1:HiMom:abcdeACXX:1:1102:1434:1000 :N:0: +TNNGAGAA ++ +F##-F!88 +@machine1:HiMom:abcdeACXX:1:1102:1470:1000 :N:0: +GGGCAAAT ++ +!FF-888F +@machine1:HiMom:abcdeACXX:1:1102:1488:1000 :N:0: +CTCATACG ++ +8F!-!-!8 diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/NN.barcode_2.fastq b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/NN.barcode_2.fastq new file mode 100644 index 000000000..3e69958f8 --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/NN.barcode_2.fastq @@ -0,0 +1,184 @@ +@machine1:HiMom:abcdeACXX:1:1101:1000:1000 :N:0: +CCTGGTAC ++ +88!!F-88 +@machine1:HiMom:abcdeACXX:1:1101:1018:1000 :N:0: +TATGCANC ++ +F8-F!-#- +@machine1:HiMom:abcdeACXX:1:1101:1072:1000 :N:0: +GTGTCTCG ++ +8-F-8-!F +@machine1:HiMom:abcdeACXX:1:1101:1090:1000 :N:0: +AAGAGCAA ++ +8F-FF88- +@machine1:HiMom:abcdeACXX:1:1101:1108:1000 :N:0: +CGTNATTA ++ +F8F#-!-- +@machine1:HiMom:abcdeACXX:1:1101:1127:1000 :N:0: +GTTGTAGG ++ +-!!F-88! +@machine1:HiMom:abcdeACXX:1:1101:1163:1000 :N:0: +CTGCGTAC ++ +88F!8--! +@machine1:HiMom:abcdeACXX:1:1101:1181:1000 :N:0: +CTAGTCTC ++ +8-8-!8!F +@machine1:HiMom:abcdeACXX:1:1101:1199:1000 :N:0: +TACTTNCC ++ +8F--8#F- +@machine1:HiMom:abcdeACXX:1:1101:1217:1000 :N:0: +CCNGCGAG ++ +88#FF88! +@machine1:HiMom:abcdeACXX:1:1101:1235:1000 :N:0: +CCTTCTGT ++ +8!F!-8-8 +@machine1:HiMom:abcdeACXX:1:1101:1253:1000 :N:0: +GGCNATGC ++ +F-!#8!FF +@machine1:HiMom:abcdeACXX:1:1101:1289:1000 :N:0: +GTAANTAT ++ +8-FF#88- +@machine1:HiMom:abcdeACXX:1:1101:1307:1000 :N:0: +GCGGCNCA ++ +!--!8#8- +@machine1:HiMom:abcdeACXX:1:1101:1325:1000 :N:0: +CCGCCGGG ++ +8F!88F!8 +@machine1:HiMom:abcdeACXX:1:1101:1344:1000 :N:0: +CCCNNTCA ++ +8-8##88F +@machine1:HiMom:abcdeACXX:1:1101:1362:1000 :N:0: +CNCCNAAG ++ +F#F-#F-- +@machine1:HiMom:abcdeACXX:1:1101:1398:1000 :N:0: +GGGATCAT ++ +F8-8F8F- +@machine1:HiMom:abcdeACXX:1:1101:1416:1000 :N:0: +ANCGGGCT ++ +8#F-!-FF +@machine1:HiMom:abcdeACXX:1:1101:1434:1000 :N:0: +AGCAGNGT ++ +8!!88#!- +@machine1:HiMom:abcdeACXX:1:1101:1470:1000 :N:0: +AGNTGGCN ++ +FF#-F!!# +@machine1:HiMom:abcdeACXX:1:1101:1488:1000 :N:0: +CTTCCTCA ++ +8-F8!--8 +@machine1:HiMom:abcdeACXX:1:1102:1000:1000 :N:0: +GCCACATA ++ +FF-FFF!F +@machine1:HiMom:abcdeACXX:1:1102:1018:1000 :N:0: +CGTGGATT ++ +-!-8-F8- +@machine1:HiMom:abcdeACXX:1:1102:1036:1000 :N:0: +ANAGGCCG ++ +8#88!!F! +@machine1:HiMom:abcdeACXX:1:1102:1072:1000 :N:0: +GATGTTTA ++ +8FF---F- +@machine1:HiMom:abcdeACXX:1:1102:1090:1000 :N:0: +TTTCGGTA ++ +!88-8F!F +@machine1:HiMom:abcdeACXX:1:1102:1108:1000 :N:0: +CATCCNTG ++ +!-F--#!F +@machine1:HiMom:abcdeACXX:1:1102:1127:1000 :N:0: +GAAACGAA ++ +F-8-8-FF +@machine1:HiMom:abcdeACXX:1:1102:1163:1000 :N:0: +NGGGATAT ++ +#!F!F88! +@machine1:HiMom:abcdeACXX:1:1102:1181:1000 :N:0: +ATTCCGAC ++ +F-8!-!8- +@machine1:HiMom:abcdeACXX:1:1102:1199:1000 :N:0: +GTGCACCG ++ +!--!FF-F +@machine1:HiMom:abcdeACXX:1:1102:1217:1000 :N:0: +TTTGAGTA ++ +8--F888F +@machine1:HiMom:abcdeACXX:1:1102:1235:1000 :N:0: +AAGTTACG ++ +FFF8!-!F +@machine1:HiMom:abcdeACXX:1:1102:1253:1000 :N:0: +CCCGGCAT ++ +!F-!-!88 +@machine1:HiMom:abcdeACXX:1:1102:1271:1000 :N:0: +AATCTGTG ++ +FF8!-!8- +@machine1:HiMom:abcdeACXX:1:1102:1289:1000 :N:0: +CCGTNCAA ++ +-F!F#88- +@machine1:HiMom:abcdeACXX:1:1102:1307:1000 :N:0: +CCGACTGG ++ +F!88-!8- +@machine1:HiMom:abcdeACXX:1:1102:1344:1000 :N:0: +GGACCAGT ++ +88FF-8F- +@machine1:HiMom:abcdeACXX:1:1102:1362:1000 :N:0: +ACGCTGNT ++ +--F--F#8 +@machine1:HiMom:abcdeACXX:1:1102:1380:1000 :N:0: +GCCGCGGT ++ +--!F8!-8 +@machine1:HiMom:abcdeACXX:1:1102:1398:1000 :N:0: +CGATCAGC ++ +-!FFF8!- +@machine1:HiMom:abcdeACXX:1:1102:1416:1000 :N:0: +GTGCCAAG ++ +F-F-88F! +@machine1:HiMom:abcdeACXX:1:1102:1434:1000 :N:0: +TTACGCGC ++ +!!FF!8!8 +@machine1:HiMom:abcdeACXX:1:1102:1470:1000 :N:0: +CTGGTNNN ++ +!--F-### +@machine1:HiMom:abcdeACXX:1:1102:1488:1000 :N:0: +CTGNTCCC ++ +88!#8F!F diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/TTGCGGCCGGTTTAAC.1.fastq b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/TTGCGGCCGGTTTAAC.1.fastq new file mode 100644 index 000000000..0339f7254 --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/TTGCGGCCGGTTTAAC.1.fastq @@ -0,0 +1,4 @@ +@machine1:HiMom:abcdeACXX:1:1101:1036:1000 1:N:0:TTGCGGCCGGTTTAAC +GTTAGGAGAGACACCCNGAAGACTNCNCACACCCTATNTAATCGGGTGCATGTCGATNAANNCTCGCCTCTGGGGNTGGTACCTATNCTTAGTTCTTGCTCCNTANACGGCGCGATTGGNCNTNCGTTAGAGACCCTGNCCTACGGGGCTC ++ +!F!--!F8-FF8-8F!#F8F8-F8#-#8-8FF!!FF!#-F--F8!!!F!F--8-FF!#8F##-FF!F88-8-8-8#FFF8-8!8-F#--F8-F--!!!-8F!#!F#F--!FFF8F-F!-#8#8#!F8!-!-FF8FF!8#!FF8--8F8-!8 diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/TTGCGGCCGGTTTAAC.2.fastq b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/TTGCGGCCGGTTTAAC.2.fastq new file mode 100644 index 000000000..0c4bdfac9 --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/TTGCGGCCGGTTTAAC.2.fastq @@ -0,0 +1,4 @@ +@machine1:HiMom:abcdeACXX:1:1101:1036:1000 2:N:0:TTGCGGCCGGTTTAAC +CTCCGACCTGNATGGATATCGTTAGCGGGTCCTGGTGAGGGCNCTCTANCGTACNGCGGAGAGCGCCCTGGACAACCCATACATCCACAGCACGAGGCTTTATGTNCTGTNTCCCGGCTCTGCCATTTTTCCANGANGTCTTGGCCCGTCC ++ +F8!8!FF8!-#8F!FF-FF88-!8!F8----88FFF-8F-F8#-!!8-#-!F8F#-8!88!F-F-F!-F8!FF8F8--FF8F--!!F!F-!8-F-F8-!F8-8!-#FF-8#!888!-88!-F!F8F-!FF!8F#F8#F--8!-F--F!8!- diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/TTGCGGCCGGTTTAAC.barcode_1.fastq b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/TTGCGGCCGGTTTAAC.barcode_1.fastq new file mode 100644 index 000000000..30f6236dc --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/TTGCGGCCGGTTTAAC.barcode_1.fastq @@ -0,0 +1,4 @@ +@machine1:HiMom:abcdeACXX:1:1101:1036:1000 :N:0:TTGCGGCCGGTTTAAC +TTGCGGCC ++ +8F!!8--8 diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/TTGCGGCCGGTTTAAC.barcode_2.fastq b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/TTGCGGCCGGTTTAAC.barcode_2.fastq new file mode 100644 index 000000000..4877e83be --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/TTGCGGCCGGTTTAAC.barcode_2.fastq @@ -0,0 +1,4 @@ +@machine1:HiMom:abcdeACXX:1:1101:1036:1000 :N:0:TTGCGGCCGGTTTAAC +GGTTTAAC ++ +8-F!!-8- diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/barcode_double.params b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/barcode_double.params new file mode 100644 index 000000000..a66be292b --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/fastq/barcode_double.params @@ -0,0 +1,6 @@ +BARCODE_1 BARCODE_2 SAMPLE_ALIAS LIBRARY_NAME +CCCCGCTT TTGCGTGT SA_CCCCGCTTTTGCGTGT LN_CCCCGCTTTTGCGTGT +TTGCGGCC GGTTTAAC SA_TTGCGGCCGGTTTAAC LN_TTGCGGCCGGTTTAAC +CACCTAGT ACTCGAGT SA_CACCTAGTACTCGAGT LN_CACCTAGTACTCGAGT +GCTATAGT CCAGCAGC SA_GCTATAGTCCAGCAGC LN_GCTATAGTCCAGCAGC +N N SA_N LN_N diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/sams/CACCTAGTACTCGAGT.sam b/testdata/picard/illumina/125T8B8B125T_cbcl/sams/CACCTAGTACTCGAGT.sam new file mode 100644 index 000000000..9d76981ee --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/sams/CACCTAGTACTCGAGT.sam @@ -0,0 +1,4 @@ +@HD VN:1.5 SO:queryname +@RG ID:HiMom.1 SM:SA_CACCTAGTACTCGAGT LB:LN_CACCTAGTACTCGAGT PL:illumina PU:HiMom.1.CACCTAGT-ACTCGAGT CN:BI +HiMom:1:1101:1271:1000 77 * 0 0 * * 0 0 GA.GTCTCGTTTATCGGGGCATTTTCTTGACTGCGTTAGCATGGTTCTCGTGCACGTATTCGTTGTCTGCTCTCTACTGCTCTTCTATGGTACAACTTCTTCATGTAC.AGTATCCCTTGA.GG.GCCCCACTCCAACG.CTTGTAAAGAT !8#!--!F!88!8---F!F--!88F-!FFFFF88F-8888FF!F8888--F-F--FFF88!8!!8F!8!--F!-!FF-!8F---!88--8!F-8-8F8F-!F8F!88!#FF-F-FF-!F!F#!8#--!-8-8F8!-8-!#!--!!-88FFF RG:Z:HiMom.1 +HiMom:1:1101:1271:1000 141 * 0 0 * * 0 0 TGATGGTA.CTA.TC..TCCCCGCTATGCCGACTGCATATAGTGTGCGCACAAGCACAGGTTTGGT..CTATTTGT..TATCCGTCCCCTCTATC.TTGG.G.TGTAATGTGCGGCCTGCTCTCTATAGCGTAGCCTAGT.GGTCTGCGTT FF88--!8#F!-#!F##F-888!!-F8F8!FF--8!F!8-8!F888!88F!F8-8F!8F!F8F-!F##8!F8FFF-##8F--F88888F!8!888#88!F#F#8FF--8--F-FFFF--F-F-F8F8F8--!8!!F88F8#88FFF-8!8- RG:Z:HiMom.1 diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/sams/CCCCGCTTTTGCGTGT.sam b/testdata/picard/illumina/125T8B8B125T_cbcl/sams/CCCCGCTTTTGCGTGT.sam new file mode 100644 index 000000000..88dca3541 --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/sams/CCCCGCTTTTGCGTGT.sam @@ -0,0 +1,4 @@ +@HD VN:1.5 SO:queryname +@RG ID:HiMom.1 SM:SA_CCCCGCTTTTGCGTGT LB:LN_CCCCGCTTTTGCGTGT PL:illumina PU:HiMom.1.CCCCGCTT-TTGCGTGT CN:BI +HiMom:1:1102:1325:1000 77 * 0 0 * * 0 0 G.TGGCCTGCATGAATTGA.CAT.AAAG.GGGTCCCGTAGG.A.C.TAC.GAACATTAGTGCAGTTT.G.CCAC.GTGA.GCGG.AGGCGGAAGGT.ATT.TTAACCTCCCCCTGT.TGTACTGATGATCGGGGGGGCA.CCGGATGCGAT -#-8-!!!88FF-8F!-8F#F-!#F---#8!F--8FFFFF!#8#!#---#--88--F8-8-8F888F#!#FFF8#!88F#FF!!#8F-!F!88!8F#8-!#88F88!!FF!F888!#!F!--888888----F8-888F#F8!--F-!-8! RG:Z:HiMom.1 +HiMom:1:1102:1325:1000 141 * 0 0 * * 0 0 ACGCCGTTGTGCGCTATTAACGCC.CTACACAATACCC.TCGTATTCTCCAGGG.ACGTTGTGGC.GGGTACCCAGAGGTGGGTATGGTTGTTGGATACAGTGGGGG.CGGCTTCG.TGGTCCCCTTACCGGAGGACCAACGAACCACCCG 88F8FF-F88F8F!8888F88-8F#!!F88-8F!888!#!8--8---FFFFF-F#8-8!-F!---#-!-F8-----8!F!!F-8F!!8!!8-!!!F!-8-FF8!F-8#8-F---F8#!F-8-8----8F888-!!FF!F8-!F88F8FFFF RG:Z:HiMom.1 diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/sams/GCTATAGTCCAGCAGC.sam b/testdata/picard/illumina/125T8B8B125T_cbcl/sams/GCTATAGTCCAGCAGC.sam new file mode 100644 index 000000000..aadbb45c1 --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/sams/GCTATAGTCCAGCAGC.sam @@ -0,0 +1,4 @@ +@HD VN:1.5 SO:queryname +@RG ID:HiMom.1 SM:SA_GCTATAGTCCAGCAGC LB:LN_GCTATAGTCCAGCAGC PL:illumina PU:HiMom.1.GCTATAGT-CCAGCAGC CN:BI +HiMom:1:1101:1380:1000 77 * 0 0 * * 0 0 GTTGCGCACGCGCGTGGGC.ACG...CGGTATTCCAACATCCGTGGTGCA.GTA.AGTAGTATGGT.AAATATCCATC.CAGGCTTCGAATCGGGCTGTGGATGTCCAAT.C.TTGTACGGC.ACACTCTACCTACTACTACCCAGGCTGG F-F8-F888F8!F88F-!-#-F8###8!!F888--8-F888!8----8-8#F88#8--8FF88FF8#-8-F-8F8-8!#88F88-F888F-FF8F!!8-8-F---F!FFF#F#F-!-8!F8-#8-888--888!8F-8-88---FF!88FF RG:Z:HiMom.1 +HiMom:1:1101:1380:1000 141 * 0 0 * * 0 0 AATGTGGCCTCTAG.T.GAATTC.GCGGGTGAGGCGTACGTTTCAACGTAGCGAA.GT.GGATGTTTGCCCA.GACAT.TTTCGATTGC.GT.CCTGT.ACGATACGTTCCTGTCAG..TGCG.AGCTG.GCGAATTCAC.CTGCTGTCTG F8-F!F88FF-88-#!#F-F--F#F!--8-8-8!-8----!F!-F-8!FFF8!-8#8F#-F8!F!FF8-F!8#8F--F#FF!8!-!F8!#-F#8!F!!#F!F88-!8!!---8-FF!##-8!!#-F!-F#8888FFFF--#!F88!8!8-! RG:Z:HiMom.1 diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/sams/NN.sam b/testdata/picard/illumina/125T8B8B125T_cbcl/sams/NN.sam new file mode 100644 index 000000000..a87a0a9a1 --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/sams/NN.sam @@ -0,0 +1,94 @@ +@HD VN:1.5 SO:queryname +@RG ID:HiMom.1 SM:SA_N LB:LN_N PL:illumina PU:HiMom.1.N-N CN:BI +HiMom:1:1101:1000:1000 77 * 0 0 * * 0 0 TGATGGTTTCGGG.TTTAGACAGTGTCATGCCTATTCC.TGGTA.TCTTTGTTAACCTACGCCTCATGCTCGAATTCGCG.GT.CAGGATAGAACTTAAAG.TCTTTGTCTGAGGCAGAGA.CGGAAG.TTTTCAGCTGTGAGGTTCCCTT 888-8F!!88-F8#!!F8FF!F-!--88!!FF8F--F!#-88F8#!!F!F!!8F88F88!!!8FFFF--F8FF88-8F88#!!#F-F88!------FFFFF#!8F!F8F-8---88-88F8#F!-F-8#!-!8--8!------F8---F!- BC:Z:GCCNAGTA-CCTGGTAC RG:Z:HiMom.1 +HiMom:1:1101:1000:1000 141 * 0 0 * * 0 0 CCTGAAGAG.C.CA.C.CCA..GGATGA.AGTGACCACGGGATGC.AGTGCCCACGATGCGTAGGACGGGGAGCCATGATCGTCCGGGTTTGGCGT.CTATCGTGATAGGAGACGGTGCCCAGTGATGCC.CCGCGCACTG.TAACCCAGT F-!F8--8F#F#88#-#-FF##F-8!-8#88-F-F-F8F-F-F8F#-8!--8F8-!F!8F!--8-8!FFFFF8F!FFF-F-8-FFFF!8--88!8-#88F!88-F-F-F-FFF8--8--!!-FFF-F!!!#FF8-FFF!--#FF-F!-F-! BC:Z:GCCNAGTA-CCTGGTAC RG:Z:HiMom.1 +HiMom:1:1101:1018:1000 77 * 0 0 * * 0 0 GGTGGGGCAGCTC..GT.CTGGGTATG.TTACATGATTCAAGCATACTGCCCCTGATA.TA.TCGCGG.TTCTGCTA.GTATTTCCCGGGAACTTCTTTCACCTATCCGAACAACAGCTTTCCCAGTCAGAGTCAGCGAACATTATAACTC FFF!-!-!F!!!!##!F#!FF8!FF-!#8!8F-8!----F-!-F8--88-FF!-!8F-#88#-8F!8F#88-8!!FF#!F8!8!!F!F-F-F!8F8FF!8---8-FFF8---8-8--!!-F8-!8888F8F8!F8FFF--!F!-8FFF--F BC:Z:CTTCGTGT-TATGCANC RG:Z:HiMom.1 +HiMom:1:1101:1018:1000 141 * 0 0 * * 0 0 CCTCG.TAGGATCATCCTCGCGTGCCATCGC.GATACT.GCTTTATAACTTTTTAATACCACCACTTAAAGC.TTAG.T.TGCACAAGGTCGTACTAAAGGACCCGCTAGCGCGTGATCTGTGGTCCCACAGAGTAC.CCGACTACT.TTA FF!8F#F88F-!F88--FF----8-F88FF8#!88-!F#-FF-8FF--88!F!FF8FF!8-F--8-!88888#!-8!#F#88F888-!--F--888F-8F-FF8F8---88!F!-FF!-!--FF--F88!-!-!FF!#!88F-88F-#88F BC:Z:CTTCGTGT-TATGCANC RG:Z:HiMom.1 +HiMom:1:1101:1072:1000 77 * 0 0 * * 0 0 CCTTGATC.CTCCGCTTGAGTTT.GTTTCAGATGCCTT.AGGAAGCGATATTCCAACTCATGGAGCGTCAGCAGCGATTGTCGTATAGCCGGGCAAATCACTAGGAATGCC.T.TGTGAACAGTGGCATTGTTGTATGGTGTGTCCCCAAG -F-F88--#F8F888-!8F!F--#-!-F8--8!FF!-8#F8-F8-F88!-F8-8--!FF8FFF-F88!!F8!-!8--8-!!!-F--F!F----FFFF!-8!8-F-F-8F8!#-#--8F--88-!-!!88-!F-!FFFF8F8F8F!-88FF8 BC:Z:CTTCCTTG-GTGTCTCG RG:Z:HiMom.1 +HiMom:1:1101:1072:1000 141 * 0 0 * * 0 0 .CGG.CTGGTACCTATCGCGACGTCCACATTGTTGTATTC.GTT.CACAACCGTCTAGCCTTCT.TACTACCGCTAAGCTTAAA.CCAACTGGACAGTGGGACACGGCT.CTC.GTCACAAACACC.ACACAGCCTGTGC..CACCTCAAG #FF!#F-8--8!-8FF-!-F--8!FF88-!-8-!-8-!!8#F8!#F--8-!8!--F88-F!F!!#88!8-F!----8888!-8-#88F-FFFF8!FF!!8F-8F8FF--#-F!#!!-8-88888--#FF8-FF---!!8-##-88!-F8-- BC:Z:CTTCCTTG-GTGTCTCG RG:Z:HiMom.1 +HiMom:1:1101:1090:1000 77 * 0 0 * * 0 0 G.ATAGG.AA.GGAGC.CCTGTAAAGTGCCGGTACATTGAATACCTCTCA.ATG.CAGAAGTAGACCAGCTTCG.CAGGACAAATTCATCATAGTTTATAGGTAATCCA.TTGAGGC.CCTTGGCTTGATATTCTCCCGTCTACCGAGTCT F#F-F-!#-8#!8---#F8!!F8-F8F-!8-!8-!8!F!F-88F88-F--#FF-#--88-!8F--FFF!8-8!-#FFF8F88F-!!--!!F!8!--88F-F8F8--!--#88!F8-!#F!8!F88F-F-F-FF8FFF8F-!!F8-!-!F-8 BC:Z:TCTCACTC-AAGAGCAA RG:Z:HiMom.1 +HiMom:1:1101:1090:1000 141 * 0 0 * * 0 0 AGAGTGGGGAGAAGCGGTGGTGTGTTTAGATGTCGAA.CATCGCCAGGTATTCGCGTGGTTTGTGGGCGC.CAC.CTCATGAGTCACAAACT.CTTACATATCTTCGGGTTTCCAGTGG.TTCGG.CGCATCGTCCCC..GGCATTGTAGC F!8!8!-!888888-8--FFF!-F!88FF8F-!F-88#!8-8F-F888FF8!88!--88FF!-8!-F!8-#-F!#!F-F!8F--FFF8-F8!#-!!F--F-!8!!-!-8F-8--8!-!!#FF!--#8!888F-!F8!-##F-!--!-888F BC:Z:TCTCACTC-AAGAGCAA RG:Z:HiMom.1 +HiMom:1:1101:1108:1000 77 * 0 0 * * 0 0 .TCT.A.ATTAAGTGCGGCAG.TGGGGCCCCCTGGTTTGAGT.AAATTGTGCGTCTATCTTACGCGGA.G.AATG.CAGGACCGGGCG.CCTGTAGGG.ATCA.CCTATCT.CGAGTAAGTGAGGGGA.ATCGGTTCTCACGAATGCACGT #FFF#-#F!!8-88-!8F888#F--FF8!FF8!F-!88-88!#888!!8F--F-8!88-F-FF-F!8-#8#88-F#-FFFF8!-8--F#-88--8FFF#F8F-#F-8--8-#!-F-8-8-8-8-8FF-#8!!888-8-88888-!--8F-8 BC:Z:AGCCCCCT-CGTNATTA RG:Z:HiMom.1 +HiMom:1:1101:1108:1000 141 * 0 0 * * 0 0 TGTGTG.ACTATCAATCGACCAGTACTTAGTTCAGCACCGCCCTACTCGGCACTGCTAGCGGGTCGACCTGGATAGCCGTAGCGCGAC.AGCGATTGTCTTGAGTGCTCGCCAGATCCTTCTGTCCTGTATTCATACA.AGTGGGAAAGGG 88!F8F#--!-8!FF8F!FF--FF-!!!--!F8F-!-!8F--!88FF!F-F---88-88-!-!!FF8!!-FF8!----!FF--888F!#F!88-8!-FF!F88FF8--8!-!8---!-888-F!8-8-F8-!88-FFF#-8-!!--F-88- BC:Z:AGCCCCCT-CGTNATTA RG:Z:HiMom.1 +HiMom:1:1101:1127:1000 77 * 0 0 * * 0 0 TTTTCTTTGTTA.GCCGTC.ATGGGTCC.GGCCCACCGTACA.ACCCATCAGCGTCTGACG.CCGTACTTCG.TACTTATGGTGACTGTGA.TGCCACGACTTGTCAT.TACTTGGGGTTGTGA.TA.TACACCCTATCCGAACTT.AGGT F8F-8!-!F8-8#!FFFF-#FF--F8!8#8!F-8-!!--8!-#-F-88!8-!FF!FF8F8F#F-FF8!88-8#--8!F-F8--F-!8F888#!!--8!F8888!F!8!#88-F88!!-F!F8!8#88#F-8F!-F!8!8!!8F-F8#88FF BC:Z:CACTTTTC-GTTGTAGG RG:Z:HiMom.1 +HiMom:1:1101:1127:1000 141 * 0 0 * * 0 0 GCTTGCCATTT.CCGGACTCTATCCGTGCTCGTAGCACAC.TATCGGCACGCCTTC.ATACACTCTGACGAC.GGCCCCTATGGAATGA.T.GTCATCTACACCCTACTCATGAGATTTTAACGGGACAGTAGGCTACATCGGGTCAAACG F!888-FF!!!#--!F-F!F!88-F8!!!!-!---!8!F8#-8F!F-!FF!F-8-8#88F8-FFFFF-!--!#8F!F!-8F!F-F88F8#8#F88888--8-88!!F-8FF8-F!F!FFF-F-F888--8FFFFF--88-8-8--!FFF-- BC:Z:CACTTTTC-GTTGTAGG RG:Z:HiMom.1 +HiMom:1:1101:1163:1000 77 * 0 0 * * 0 0 TCCT.CA.TCGCACCGGAGAATTCCCACGATTCCCAAGC.AA.ACGATCTAATCTGAGCTTAGAACGAACAGACTCGGTAGGGGGATATTGTATCGCTGCCGTCGCGTGCTATGCTACGGTCTC.GTTATAATGGC.TTTTGGTCGCTTTA F8F8#-8#-8F88!F--88F8--!8!F8F8!!F!!FF-8#-F#FF--F!8888-F!--88-888-!F8F!8FF8--8!FF!888!8--F8F-F8F!-!8---88-F8F-!!F888-88F8!F88#F-FF8F-!!8-#!F!-!88-!F!888 BC:Z:TGTCTATT-CTGCGTAC RG:Z:HiMom.1 +HiMom:1:1101:1163:1000 141 * 0 0 * * 0 0 GG.GCGC.CTCCGCACGCCA.TAGCA.CTTG.GTAGGCCCTT.TTTCCAGTTTCTGGTAGGTCTCGAGGCGTATCGTTT.CGGCGTCTTTCCACTGAAAGGGGGTCTTAGGATGGTATCTGGT.GCG.ACGTGAGTGTATCGCACGTACCC F8#!8-!#8!8-8!88-!!-#8-!8F#8!!!#F!F--!!---#-!---8-!-FF!8!!F!8-8!!!F!--F!888!F--#F8F8-F8!F!-!8F8!-F--8!F!F8FFF!F-!!FF-FF88F8#---#8--FF-!!F!-F8!F888-FF!! BC:Z:TGTCTATT-CTGCGTAC RG:Z:HiMom.1 +HiMom:1:1101:1181:1000 77 * 0 0 * * 0 0 CGCGTGAAACGTCCACAATAG.GACGTCGCGTGATGTTGTTCTA.GGCGATAC.ACGAGGTGATCAGAAC.CCTTCAGTTTGTTGGAGTC.CTTCTGGACACC.CACCCGGATGATTAAGAGCTACGCGCTAGCCATATACGA.ATCC.TC !8-!88888-!F8!888F!8!#8--F!F!--!-F!-F-!8!F88#!-!----F#---F-8F!8!-8-8--#8-F!F88-!-!F8!!-!!F#8F--F8FF-8!-#-FF-FF8F!FF-!FF8-8---F!F8F888!!--FFF---#888!#!- BC:Z:TGTGTCAG-CTAGTCTC RG:Z:HiMom.1 +HiMom:1:1101:1181:1000 141 * 0 0 * * 0 0 CCAG..ATT.GTACATACATTCACTCA.GATCCG.CGATACGGTACC.TGTCTATTGA..AGTCACCGTCGGTCGACACCGTAGACCTGGTACGT.ACTCTGTAT..CATAGTTTAGT.AGGCGTTG.CGGA.GGATTGGCT.GC.ATTCA !FF!##F--#!-F8--F!-!---!F-F#--8-F8#F-8!-8!8!F8F#!-F--8-F--##FFF-8F!!!FF!-8-FF-8!F8-!-88-8FF8--F#8-!8--!-F##FF!-888F--8#F8F-!!!-#F!-F#---!!FF-F#!8#88!-8 BC:Z:TGTGTCAG-CTAGTCTC RG:Z:HiMom.1 +HiMom:1:1101:1199:1000 77 * 0 0 * * 0 0 .ACCCC.GGTGCTCAAAA.TTGTAGTCTGGACTGAG.CGCGGAGAC.TGGTGGTTGTCCACCGTCG.CTTCCGCTGGCGAATTCTCATATT.TGC..CAGATACGGGTACCA.G.ATGTTGGTCAAA.CCCTCGTCCCACGCGAC.GAGAA #-F!FF#F!88!8!88-F#-!-F8-!F-8-F88!F8#-!F!F8---#8!--8-!!!!F8-FF8!8-#8F8-F8F-!!-F8F!-F8--!F-F#-!-##FF--!-F8-F!FF!-#-#FF-!888!FF8F#-F8---!8F!88!!8F8#8-88F BC:Z:ATGTCNTT-TACTTNCC RG:Z:HiMom.1 +HiMom:1:1101:1199:1000 141 * 0 0 * * 0 0 TTTGAAATAATTGGGGC.GAAAAGCTTGCAATGTGAACTAGGTATGCATG.CA.ACG.GCCGTGCA..T..TTTCCGAGATTGATGCACTGCGAATTAATGACTAGGGACTGAC..CGCCCCGCGTCCGGTCCTGTTTGGGAGGTAATTTA !F-FF---8-!F88F8F#--F8-F-8F-88-8!-F-88F-!FF8!F-8!8#!-#F!F#8--F----##-##!-!8-8--8-F-F-!!F8!8-F-F8F--8F-F8-F---F!8FF##88-F---!-8!!-!888-!!F8!8F-8!--8!!F8 BC:Z:ATGTCNTT-TACTTNCC RG:Z:HiMom.1 +HiMom:1:1101:1217:1000 77 * 0 0 * * 0 0 CCATCGTCAAGAGGTGCGTGGCACAAATATCGACTGATGTAGCATA.GGACGATGTTCA.GCGGTGGCTGCAAGAACACCTCCATCTGGGATATTCGTGTCTTTT.ACGCGCGAATGGTTTC.CTACTGTCCACGTACACTTGCTTCACCA !---!!!F-888-!8---!8!88-FF88-F-FF8-8FF8-FFF--8#-!-8!FFFF!8F#F!FF!!F8-F--F!FF-FF!8!8F88!8!8F8F8-F-F-!!8!8-#-F8FFF!88!8-!-88#!FF-F8-!FF!8!8FF-F-8FF8-F-!8 BC:Z:GCGAGGCT-CCNGCGAG RG:Z:HiMom.1 +HiMom:1:1101:1217:1000 141 * 0 0 * * 0 0 CCCTCCTCTCAATTATTGCTCTCATTCTCC.ATTCGA..TTACGTTCTAGACGGTCTG.CAACCCGATT.CGTAA.AATTGCGGGATCTTCTAATCATTAGTCC.GAG.GGCGTTCCG.TGCTCCGCA.ACAGTCGGATCC...AGTTGCC 8!F---!8-8F8FF-!-FF!-FF8!!!!!F#-FF8F-##-!8!88!F!88F-!!8!!!#F8--FF!FF-#-88--#--F!F--FF8-!!F8!8F-!--FFF8FF#-8-#!-!F8F!-8#!--F8!FF8#8!8F-!8FF8--###F-!F--- BC:Z:GCGAGGCT-CCNGCGAG RG:Z:HiMom.1 +HiMom:1:1101:1235:1000 77 * 0 0 * * 0 0 GGTTTAGGCCACGAC.CGTTGCCG.GGGGTCGAGCTTTCTA.TCATGGCTTTGTCATGTCGCTGCCATGGACGACAGTCCGGACTCGGGTCCGAG.GC..GGGCGGT.CTC.GGCATCGAACCAGGTATCTAAGCGT.TCAGGCAATTCAG F-!-F8-8!F--F88#!F!-F8!!#!-!8!!FF!-FF8F-F#F8---88!!F8!!888-8888FFFFF-FF--FFF-F8--8FF!!8!-8!!---#!!##8-888!!#!-!#F8!F!!FF8--F-8!--F!---F-8#8F-8F-8--F-88 BC:Z:CCATCTGT-CCTTCTGT RG:Z:HiMom.1 +HiMom:1:1101:1235:1000 141 * 0 0 * * 0 0 GGTACGATTACCA.CC.TAGTTTGTTCCGAG.C.ACCCGAG.CTCCGCG.ACCGGGCTAGGTTATTTGCTTACTATTATAGGACTGGGGCGTTGGGGAGTT.CCAA.CTAAAA.TGTGC.CAGTGC.TATCTACTCACTAAGTTGCTCCGT -!!8!--8--F!-#!8#-888-!F!8-F!8-#!#F---88!#!8-!F88#F-FF-!F!-8!!8FF!!8-!-----8FFFF88F8F!!F!-8F!-!!---F8#8--8#FF---8#!8888#8F!-!F#8--!8-8-8-FF-88-8-F--F8F BC:Z:CCATCTGT-CCTTCTGT RG:Z:HiMom.1 +HiMom:1:1101:1253:1000 77 * 0 0 * * 0 0 .GTTGAG.AGTCCCTA.TGAGGCATTTCCAATC.TTCGGTGG.CGCTTATCGGGTGGGGATTCGATCGGGAATCGCGCA.C.CGTCAGTGTATGATTC.A.ATCGGTGCGTTC.TAACTTGG.CTATGTCC.CGACA.CCTCGGTCTGCTT #!F-88F#8---F8F-#-F8F!-FF8!8!-88-#-8!F-F--#FF!!8-8F!8F!!F!F8F-88F!--8!8FF!F--!F#!#-F88F!8!F--!8FF8#8#F!-!!FF!-8-!#!-8!-F!!#!!88F8-F#-FFF-#F---!F!!F!!8! BC:Z:ATTGGTGA-GGCNATGC RG:Z:HiMom.1 +HiMom:1:1101:1253:1000 141 * 0 0 * * 0 0 TTCGATG.GTAACGTGCTAGCTAACAG.CTCA.GGTCCCCGCCTTTCCCTTTAG.CGTC.TTCTCCCCCGTCCTAAATTGCGCTTGGAT.GCGGGTT.GGT.TCACGGCTACTCATTCTACAATGACT.G.TATGGGGCATTCCATAAGG. F-8!--!#!8F8!F!!F!FFF-8-88!#!-!F#-F!8!88!-88--8!-8!-8!#F-F!#!!!F!F8!88F8-F8F8F8-F---88!F-#!FF8-!F#F8-#--8!F!--8-F8-!-8--8--F8F8!#!#!8!!8!88F-F8!F88-F!# BC:Z:ATTGGTGA-GGCNATGC RG:Z:HiMom.1 +HiMom:1:1101:1289:1000 77 * 0 0 * * 0 0 TTCCGAGGC.CCGTACTTTTCTA.C.CCC.CT.TGCGTGTTATGCGTAACGTGTCTGTTA.TG.CCCGTGAATTAGGAGCGAGCTACTGATGAGGTCGTCCGGGGCGCA.TAGACCCCCTTTTCT.CTAACCG.GAATGGTATGCCTG.C. 8!!8-F-F8#!F8!-!F!8F88F#-#!--#-8#!--8-F!-8-8-!!8F!!F8F-!8F88#-!#8!8-888F!-8888!-F--8!8-F8-8F-!-88-8F8-8888---#!FF-!-!8FF-!8-!#FF-8!-F#F-8!8!FF!-F!-F#!# BC:Z:CCTGTCCG-GTAANTAT RG:Z:HiMom.1 +HiMom:1:1101:1289:1000 141 * 0 0 * * 0 0 CATTTTCGT..T.ACAA.GCTCTAGT.GGGCA.CAGGCGGGGGGACTAACTTAGGAACCCG..GAATTCAGGACTATCTGCGTACG.ACAG.GGTTGCAGTGACGGGAGAAG.CGC.ATCGCT.TGTTAGTGTTCCTGC.TACAGGGCACG --8!!!!-8##8#8!F8#!-F!!F-F#-F!-F#--FF!888-8!--!--88-FF!-8!!8F##--F!--FF-F8-F8!!8!8!--F#F---#-!-F--FF88F88F!8!88-#!8!#8F8!8-#!8--8-!-!-!-!8!#--!--!-FFF- BC:Z:CCTGTCCG-GTAANTAT RG:Z:HiMom.1 +HiMom:1:1101:1307:1000 77 * 0 0 * * 0 0 GT.GTATGTACAGAGACTGTGTCGTTTAGTGGGGTT.GGAGCGGCCG.A.TCTTGGCCGCGC.G.CCCTTGTTCTACCGGCAGCGTCAGCTCGTTTATCACC.AC.GGAGTCTGCGACTTGTTAGG.CA.TACCTATGAGAGCGC.CGC.G 88#-8-8F!8!8F-888F!F-FF-!-F8-!8!8!-8#!-F8!!!8-!#F#-F8!FF!!-F!8#F#!!F8!FF-8--8F!-!FFF888FF!8F!!!-F-!8-F#88#---F!-F-8-FFF!8F-8FF#!-#F---8F!F8--88!!#8-!#! BC:Z:TTTATTGC-GCGGCNCA RG:Z:HiMom.1 +HiMom:1:1101:1307:1000 141 * 0 0 * * 0 0 AATTG.CTTTGAGATAGAGGGCCCCTACGGTTGTCTA.TACTCTGTGCCAGAAGCCCAGTCGG.CGGGCAACTTTCCGGCTCCGGCTTTTG..CGCGATGCA.ATTT.GTTTGAGGCGCTGGTTCCCTCACTTCAGATTGCC.ATTCAT.C 8F!-F#F-!88F8-F8!8F!!!-!!8-F--F8-888F#8-8-!8F-!!-88-8!FF8FF8!88#8-88!-F!F88F-F--8--F88!8FF!##--8F--F!F#8!!8#--!-8FF88!-!-!-F!F!F!--!-!---FF8-8#8-F88F#! BC:Z:TTTATTGC-GCGGCNCA RG:Z:HiMom.1 +HiMom:1:1101:1325:1000 77 * 0 0 * * 0 0 AACGCCTTTGGATCCCCTCCACGGAGGTTACAGATTAGTAG.CAGGAC.C.AC.CGAAACGAGTGTTCTGTGAGGGTCATC.TAACG.T.CG.GCAATGGA.ACAAACAACAGGATTAATCGAGCTAACG.ACCT.GATGGTAGCGAGCGG 8--!F-8-!888FF!FF!!!8F-88F!-88---8F!--8--#F----!#!#F-#8--88--88!!!8!F88-F8-F-!F!8#-FF-!#F#-F#---FF!FF#----8-F88F!!8FF-8!---F-FF8F8#F-!F#8F!!8-F-!!8--88 BC:Z:TGTCCTAG-CCGCCGGG RG:Z:HiMom.1 +HiMom:1:1101:1325:1000 141 * 0 0 * * 0 0 CCAGAACATCCCCTGGAGCCTGGTCTACT.GGGGACAGGGTGTGCGT.GCAC.GGG.CGGTTCGATGGGGGAG.GGCGGGACTCCTTCGCAGCAAAAGAACC.TAATTTTTACCTTCCTTTTGTGAAGTGCTAGCTA.GTTCGGG.T.TCG 8---F-F-F-!8!!-!-8-F888!F8-!F#F-!-8!8-!-F8---F!#-F8F#FF8#88!-!!FF8F8-!F8!#8F-F8-88F!--F8!F--8F--F-F--!#F-F!!FF-FF8!8!!--F-!-!8F8F!!F-!-!8#FF8!8--#F#!!F BC:Z:TGTCCTAG-CCGCCGGG RG:Z:HiMom.1 +HiMom:1:1101:1344:1000 77 * 0 0 * * 0 0 CACTTCT.GTTCACA.GGGTAGCCC.TTGTTTCTTGTT.TTCGCATTGATCTTTTCCGGGTAGCCAATCA.CGGTACGGCCCACGGCGTTTCATGTTAGAGT.TGGGGTACAACATCCCTACGCTGTCCACGCTTTGGCACACT.CTATCA !FF!!-F#!8!-F--#F--88-F!8#-8!-F!!FF!-8#F-F-!F!F8--F-----8-!FFF8!88F-8-#!F8!8!8F!-!8F-8!!!FF--F8FF8!FFF#!888F-888F!F-88FF-F-FF!!F!F!!F!!---F888FF#8-8F!8 BC:Z:TTATCTGA-CCCNNTCA RG:Z:HiMom.1 +HiMom:1:1101:1344:1000 141 * 0 0 * * 0 0 .CGAGAACGCCTTCGGTCGATCTACTCC.GATGCTTTAGGAATGCCATT.CG.TGCCTT.GCTATTACGTGCCGGCGGCCGTTTTCCAAGTGCTATTA.CCTTAGCGGTCCCGTCTCATGTCACGGAGAAGAGCTGTTACTATGACGGTGG #FF-8F--8!8--F-FF8!8!-!88F!8#!8F-8!---F-F8-!!FF--#!F#8-!!!-#-FFF8-FFF8-8!-88!!8!F8-FF!88F!8!8---8F#-!FF88F-FF8!-F--8-FF!888!!!-8-F!FF!!88-8-F8F8-8FF!8- BC:Z:TTATCTGA-CCCNNTCA RG:Z:HiMom.1 +HiMom:1:1101:1362:1000 77 * 0 0 * * 0 0 GGGTTAGTCCGC.G.CTG.T.CCTGCG.CACACGACT.ATCATCCCCCG.TGTTTGGTTT.TTGTACG.A.CATTC.GTCTCAATTCGGATTGGCGTC.TAG.AGAA.TAAC..CG.CATCTAT.ATCTA.GCCGTAT.TTGGTTCTCCTG --8-!--FF-!8#!#-FF#F#F!--88#-8-F8F---#888F888-!--#!F-88-8F!!#F8888-!#8#888!F#88!F8FFF-8-88F8!!FF8!#F8-#--FF#8-88##!F#!-8!-F8#8!F8F#!F-88-!#-!--F-8F8F8! BC:Z:NAGGTNTG-CNCCNAAG RG:Z:HiMom.1 +HiMom:1:1101:1362:1000 141 * 0 0 * * 0 0 CGCTATTGTAACGATCGTATTTTACTT..TCT.TCGCACAGGGTATAG.CCGGGAGGAGG.TACGGCCTC.AGCCGTGCGCGCAGG..GGGCGTAATCCTTATGTCAAAATTGCT.CACTAC.ACGTCTAGCAAGCATCAGGAGGAA.AGT F!-F8F!F!8FF-FF8888!!-8-8F!##!-!#-!8F-88!-!!--8!#F--!F-FFF--#!8--!---8#8FF----8-F-F-!-##!F8F!88-F-8-8-!F-8F8F-F!!8-#!FF8F8#88F-F8F8!--F!F88F8FFF-8-#--! BC:Z:NAGGTNTG-CNCCNAAG RG:Z:HiMom.1 +HiMom:1:1101:1398:1000 77 * 0 0 * * 0 0 CTCTCTT.TTTCTGCTGAAGACTGCGGTCCTTATGAATT.ATTTACCTGTACCCAGTTGTGTTAGGTACATG.TTTGCA.GAACAGACATTCGTCGCCCAGCTACCGTCACTCCGA.AAGGTTAACCTGAGATCTG.A.AGCA.GCG.ATC ----88-#FF!-8F8--8-!F8!--8F8!F!88F!----#-8!F8FF8FF---88!F8-88-8-F-8888!-#F-F--8#!F---FF8F8FFF-88!8F----8-888-F8888FF#F-8!--8F8!-888F!!-!#F#--F-#8FF#88! BC:Z:NCATNCTC-GGGATCAT RG:Z:HiMom.1 +HiMom:1:1101:1398:1000 141 * 0 0 * * 0 0 CGTCCTGTACGTGTCGTTAAACTGTC.C.GC.TTGCGTA.GGTGCCGTGCACGGTATAGCACGTTGGCATGGGCGAGCACTCACAACACACTGC.GGG.GGGATTGGCTGAAA.GGAGCGTCGTTAAGGGCGCTAATGACCATGTC.CAAA 8F8---!-F!F8F-F88-F--F!8!!#!#88#!!F--88#-F8F8---888-!88FF-!F-8-F--!!-!FF8F888--88!--8F88F-8F!8#-8F#!FF8-!F--!88--#!88F--F!888F88!8F8!FF-!8F8-8!F8!#F8FF BC:Z:NCATNCTC-GGGATCAT RG:Z:HiMom.1 +HiMom:1:1101:1416:1000 77 * 0 0 * * 0 0 AACTTGGGTGCCCGC..GCTCTCGAGGCT.G.ACGTCATGCTTCG.TACGGTTACGCT.CTGGATCGGCACCTCAGT.TAT.AATTGGAGCCCAC.GTG.CGGATATG.TG.TGCGGATT.CAT.GGT.TGGCGGCAGGGAGCC.CCCATT F-!F-8!-!F88-8!##!!---F!--!-!#-#F8-8-FF--8F8!#--FFF8-F-8!-#8!88-8F-!F8-F8-F-8#!-8#88-FF-8!FF888#!88#F8!8FFF8#!F#8FFF8FF8#8-8#F-8#--!F8!-FF!88!!-#!--FF! BC:Z:TAGCGTTN-ANCGGGCT RG:Z:HiMom.1 +HiMom:1:1101:1416:1000 141 * 0 0 * * 0 0 TGGTCCTCTGGTCAGCAGTTCTAAGTGCCGTCTATGG.TGGGT.CACCA.CGCTA.GT.ATAGGTCCCTAGGTCGGGCGTGCGACTCACCGCCGGAAGGGGTGGCCGGG.TATTTCTTCCAGGCAAGCCA.CTAATGGTAAATCTGTCGCA -8F8F-!-!--F!F8-F-!F888FF-F--F8!--888#888!!#-F-!-#F-8!F#!!#----!8-!!88F8!!F8-888!FF8!!88!8FF8!---F!F88!8-8F88#-F----F--8F-!FFF!F8-#-!-F!F88--8--!-8-F8- BC:Z:TAGCGTTN-ANCGGGCT RG:Z:HiMom.1 +HiMom:1:1101:1434:1000 77 * 0 0 * * 0 0 TACTC.GTGGACTTGTATCC.GGACTTTCTCTCTG.TACTGGGTT.CGCCGAACTCCCCGTT.AGCCATC.CGGTGCTGGACCACA.ATCGCGTC.GACATGCGCACTAG.CGAACCCTATACTCTA.TTC.CCTTCGCTTCGGCAGTTGT -888!#8FFF-F!-8!F!F-#!8-F888F8-8F!8#!FF!!8-!-#-8F!!8F8-F88!-F!#-!8-88!#-F8F88!F8-!F-F8#F!F!F!--#8-8-!F8!8-F-F-#FF8F-F8!-!88-!8F#!!8#88-8!F!!8F8!-F88!FF BC:Z:AATTTGCG-AGCAGNGT RG:Z:HiMom.1 +HiMom:1:1101:1434:1000 141 * 0 0 * * 0 0 TTTGTTTCAGGGCCTTTGCCGT.CGCA.TATTGTGTCTCTTCCCAGCAGCTGTCCTTAATGAT.TAGCAGATCGCCTGTGCATTA.CGCACCTC.TCGTA.AGGGGTGTTCCAACGCATACA.CTGC.TGG.CGT..CAATGAATCAGATT --!!F!8!FF-!-!88!88!-!#8-FF#F888F!!F!8--8F-!FF8-!F-8FF!FF8F8!88#8--!888!-F!FF8F8F-F-F#!F!88F-F#8!!F8#-!8!---88!--88F-F-88F#8888#-F!#FF!##!F8-!-8F8F-8F- BC:Z:AATTTGCG-AGCAGNGT RG:Z:HiMom.1 +HiMom:1:1101:1470:1000 77 * 0 0 * * 0 0 .ATCTTTGGGATCATGAATTAAGGATTGTCCATGCGACAAGC.ATGTAC.ACAGCG.ACAGAATTG.TACGATGAACGTCGTAGTTGCGTTACCAAGGCACTAG.ATTACCCTCT.GGCCTCGATTCG.CCACCCTCTTGG.GGTCCCGAG #---FF8F888-F8-8F-!8F88F88FFF-FFF-!8F!F-!!#-88F--#F8888-#F8F!FF8--#!-8F88-8FFF!F8-F!F8-FF!88--F-F888-8--#8F88--FF8F#88-8-F!-F8-F#F8-!8F!F--F8#-F8!8-8F8 BC:Z:GANCGAAC-AGNTGGCN RG:Z:HiMom.1 +HiMom:1:1101:1470:1000 141 * 0 0 * * 0 0 GGGAATTCCGGTTTTTGGCGAAGTCTCGATAACTTCCGCGCGGCACCTAACTTGCCAGCTGTGGTTCGCGTCGTGA.TTAATGTTGGG.TCTCGC.CGACATAAAA.TGTAAAGGGAGGCCTTGGAGGCCC.GGTGTATGCT.CCAGCTGG --!-8F-88F-F---!8!F--8FF!8F--!---!-888--8F-F--!8FF!8-FF!8-!8-!----8-!8-88FFF#8!-8!-!-F!8#-8-!!-#8F888F8FF8#--!888!8F8!F888!!-F8-!-!#F-888F!8!-#F!F8F8!F BC:Z:GANCGAAC-AGNTGGCN RG:Z:HiMom.1 +HiMom:1:1101:1488:1000 77 * 0 0 * * 0 0 GGTCCTGTTTATGCGTTCGCTGA.G.TGA.ATCACTGCCGGATGGCTT.ATAGGTTG.GT.ATCTTACTGCGGGGCACTCAAGTTCCGCCCAAGCA.GATTGGATTAAT.CAGAA..ATG.CGGT.CCGCG.GCC.TGTT.AATTTCATCT --!F-!FF-F-8FF!!F!F!--8#8#FFF#F!!8!F88-!F8FF!-!-#-!8!F!--#!-#8-----!F8!!!F88F-F8F-8FF8!F!8---FF-#--F-FFF-8-8F#FF88-##88-#FF8F#F----#-FF#8!--#-F-F8FF88F BC:Z:CGTCNTGT-CTTCCTCA RG:Z:HiMom.1 +HiMom:1:1101:1488:1000 141 * 0 0 * * 0 0 GGGGGTTAACCTCGTGT.CGTA.GACATATTACACGCTAGGACCGCAGGTGTGGAGCG.T.TCT.CGCCGAAGGCTTTAGGTG.C.AATCTAAATCTGTTGCTGATCTTA.GCGCAT.GTAT.CCGTGTATCTGGAGTAAC.CATAGGTCT -8--8F!F8-F-F!F-8#F--F#!8F--FFFF!-!!F!F-8F!8!FFF!8--8!F-!F#8#-!8#!8F-FF8----F-8--!F#!#888-8-8FF!8!88---888!-F8#!FF!-!#F!-8#-!F!8F88---!8!8-8F#-8FF-FF!8 BC:Z:CGTCNTGT-CTTCCTCA RG:Z:HiMom.1 +HiMom:1:1102:1000:1000 77 * 0 0 * * 0 0 CTTTTCGAGCATCGTACCATAG.TGTACGTCGTGTA.CCCTAAGTGGCGGACTCCCGCCTT.GGACGGGTGCCCGTTTACCCACT.AACCACACCTGAGTACCCCACGGCGCAGCTCTATTGCTGTCCTCTTCTGC.TGAT.TATTTGG.A --FFFF-FF-8-!!--!88F--#8!88--8---!-F#!8F-F8F!!!8!88--FF--F-F-#8-8-!!88-!8F!8FF-F-F8F!#---8F88!!-8F-F--8F-88!-!8-F!88FF-!88FF-F88!F-F!!F-#-F88#!88-!-!#F BC:Z:AAAGCGAG-GCCACATA RG:Z:HiMom.1 +HiMom:1:1102:1000:1000 141 * 0 0 * * 0 0 GG.GTTCTGTG.CTCTTGAGCAGTGCAGCCCGCGATGCGCCGCGCATTCATTCCATATCGGTTT.G.ATA.CGTTACGCCTGCGTCCGCGGC.CCTGATGTCCTCGG.AGATTACGTGGTAGCAACATCAT.TGCATTTGTCGCGGATTTT --#!!F----8#88FFF-F--8!---FFF-!888--!8!F-FF8F8FF888!-F-F-FF!!FFF#8#8--#-F-FF8F-F!F!-8F-F-!-8#-8F88-8-F8!F-F#FFF!-FF--!8-F!F-8-F8FF-#!F!FF-FF88FF-F-!F88 BC:Z:AAAGCGAG-GCCACATA RG:Z:HiMom.1 +HiMom:1:1102:1018:1000 77 * 0 0 * * 0 0 .GGAAA.GGATAA.CCAGACACCCAA.GGATATGTAGCATTGTTATACCGATCCTTGCCGCTTTTTGGTAAGCAGAGGACCATACGGTAGGG.GTGACCATGCTTCAGTCCCGGTTATATGCACTGGGCAGACGGCTGTC..CTTTCGTCA #F---F#-!-!--#F88F8FFF!8-8#F-8-F---F8!F-F!!!-8-F-F88FFF888F!!-!8F!!!F-F--F-8F-F!F88F8!F!F8-!#!FF88-8-8-!!F8!-!8!-!!-FF-----F8--!88-8-8F-F!--##F!F-F-!-F BC:Z:TCGTNTTG-CGTGGATT RG:Z:HiMom.1 +HiMom:1:1102:1018:1000 141 * 0 0 * * 0 0 TTTCACCAGGCCTCCTCGTAAGTAGATCTTATTTGGATCCAGGTAGCATCGGGGGAGCCGACATT.GTCC.GTCTCAGCGTCGTCCACCTACTCTGACG.GTACCAGAGTGCTCCCGGTACCTCAGTGCCAAGTCGGATTAGCTTGCCAGT 88!!8-8F-F-F-8-!!-!F88F-F-8!FF-8F!8!F!8FF-FF88-F8!F!!8-F!F8FF8FFF#!8!F#8888!-8-!!F-F!F-F8!-!88!--F-#!F88!F!-!F!8-8F!!-!F!--F--F8-!8888F!!8F88!!----!888 BC:Z:TCGTNTTG-CGTGGATT RG:Z:HiMom.1 +HiMom:1:1102:1036:1000 77 * 0 0 * * 0 0 CAGTGTTTGTTCGAATCCGCTCCCTTCTGCTGACGTGGGT....GG.AACCGAAACGCTTTTCTCCCAC.CCGG.GTCGTTCAACTCTA.ATGGGACAGCGCATGGTTCGTCTA.GC.TGACTCGTGGCA.ACGTCCTACGACCGCTAAAT F-!8--!F-F-8!F8F888!!!F8!F-8F!!F-F-F!-!F####!!#-FF8!F-F!8FF--8F-8FF-!#!--F#FF-!8FFF---F!-#8-F!!8!--F!FF8-88FF8--88#F-#!!-FF!F---!F#8F--88!F-!--!8!8F8-8 BC:Z:NCATATCT-ANAGGCCG RG:Z:HiMom.1 +HiMom:1:1102:1036:1000 141 * 0 0 * * 0 0 TTCCTCG.ACGTCTTTG.AGA.TTTCGCCCAAGGCTTGTCC.TGCAAGACGTCCTGTCGTATAAAC.GCCACGGGCGGCTAGGACTTGGA.ACGGACCT.ATAGTTCCTGTGCCACTT.TCG.GTTTTCGTCTTGTTG.TGCGA.AGGGG. F-!--F-#-8-F!-F--#-!-#88888F-FFF-F!8F!--!#-!-88-F!!F8!88-8-!8--F88#-F--F8FF!-F!!8F8FF8FF-F#--F-F8-F#F-F!F!!FF8!!F!88!F#!-!#-!--F8--!-8!8-8#F88-F#-8-F-# BC:Z:NCATATCT-ANAGGCCG RG:Z:HiMom.1 +HiMom:1:1102:1072:1000 77 * 0 0 * * 0 0 GCGCTTGTTCCGATTTGT.TGGCGCTGCGGCAGCCTGATCGG.GCGCCTTGGT.GAGAGGCGCACTTGCACTA.CG.CGGGCTACCGCCA.ACGTTTTCTCTGCCGG.AGCCGTATCCGGTTGGAT.TTCCG.CCATCCACGAACTTCATC F---F!!-!8!F8F8--F#8F-8888!!--F8!-88-F88FF#!88F-F-FF-#FF-F-FF!-F-!FF!8--F#-!#F8FF-F8!FFF!-#F!F8F8!8FFF8!-88#--8!FF8F-8!F8-!8-F#8-!--#FF8!!--!!FF8FFF8!- BC:Z:CCCATGCC-GATGTTTA RG:Z:HiMom.1 +HiMom:1:1102:1072:1000 141 * 0 0 * * 0 0 A.GAGGC.CCGCCCC..TT.CTCGT.GCCCTCCCAACCGTGCGACTGG..GCGCTGGACATCGTCGCAACTTACGGCGTGTGCCCTGAAGGTGACTACACCG.TGAAAGG.CGCCTCGCCGTCCATGCCACAAGGTGGACG.TCATCG.CT 8#--8F-#F8!F!F8##88#-!F-8#F!-F---FF-F8-!8-8-8F8!##--F-F-8FF-FFFF--8--!8--F--!FF!!-!888FFFF!!!-!--F-8!-#--8FF!-#FF-!8F!-F-!-!8-888FFFF-8!--8!!#-F-8F!#!8 BC:Z:CCCATGCC-GATGTTTA RG:Z:HiMom.1 +HiMom:1:1102:1090:1000 77 * 0 0 * * 0 0 GCCTACGCATCCGCCC.CACTG.ATGGGTGAGCC.G.ACTAAGCTGTAGTGCCTGATCCCTCCAGGAGCCCTTTA.TGAATCGGAACGCTATGCGACTTGTGATAACGAAAATTTCAGAAGTT.ATCGCCAGTGTGGTTCTTCC.AACATG !-F-88F88!!8!--8#---8!#F8F8-!F--8!#8#8-8F-8-!-F888FF8!8F88!-F-F8!8F---!F8!-#8F-F8!F--8F!!!8-F8F8FFF!!!---8!-8FF8F!-8-!FF!F-#-FFF88-8!!8!!8-8!F-!#FF!8!- BC:Z:TTGCCTTT-TTTCGGTA RG:Z:HiMom.1 +HiMom:1:1102:1090:1000 141 * 0 0 * * 0 0 TGAG.AG.CGTTTTTTG.CCGCTACCTTG.GGTGTGCGTGCCTAGGCACT.AATCTCCCGCTGTTGTAGGTCTATGTATTC..CGTGATGCCGC.GCTGATGCTGT.TTCTGCGTCGC..GCCTGC.CCGTTGCATATCGTGGCGGTAACA !FFF#F!#-F8F-8-!8#8F!8F--!-!8#!!--8F-F!F!-F8!--F8!#F-!8!F-8!FF-!F-8--!8!!FF!!F!-8##!---8!8!--F#!!F--FF--8-#F!F--FF!F8-##-8F---#-88!--F-FF8!FF88-!!F8-!F BC:Z:TTGCCTTT-TTTCGGTA RG:Z:HiMom.1 +HiMom:1:1102:1108:1000 77 * 0 0 * * 0 0 TTA.GGGGAGTGC.AAGG.CTTA.AGTTCACCGAGCCCATAGCCTC.TGTTGTTGCG.GGGGGGTTCCTGTGCTGCC.TTGCGCAGAGCC.GTTTATGCTGAGGT.GCGGAAGACCAGTCAGT.ATTGATGGGGGTGGGAGAGGGAA.TAG 8!F#8-8!--FF-#8-!!#8F--#-F!F8-!!!8F!FF-88!-!8F#8-F-8!888F#FF!88!8-8!-!!FF!F8F#!-8-!!-F8-F-#!!!F-F8FF-FFF-#-!F--FF8-!-F!--F-#-FF!F!-F-8F8---888--8F-#8-8 BC:Z:CCCGNGCT-CATCCNTG RG:Z:HiMom.1 +HiMom:1:1102:1108:1000 141 * 0 0 * * 0 0 TTTTCCAGTC.TTCTTGCAGGCCGGTGCATCGGCTT.ACGCAATG.CCCCTC.ACGTTGTGAGTGTCCCGATCAATTTG.GC..AAGTACCAAAGGTGCCTGTCTGTAGTTGAACATTACGTGGCGTATGG.GTAAGTTTCTATGCACGCG 8FF-8F8-88#F8--8F!F--8888F-8F!!--!8-#8-8-8--8#8-8F!F#8!F-F-8!--!8-!!8!88!-F!!8-#--##F--8-!-8-F!FFFF88!8-8FFF-!F8FF8FF-F!--F88-!-!!8#-F88!F8F!8-F-8-F--- BC:Z:CCCGNGCT-CATCCNTG RG:Z:HiMom.1 +HiMom:1:1102:1127:1000 77 * 0 0 * * 0 0 GCC.AACGATCTT.TTTGCTC..CGTG.TGCTTGGTCTTCTTGTCTCTAACTA.CGTGTAGTGAGAGT.TCTCTCTCGAGCGT.TCTGGATTGC.CGACGGACGAGGAATTAGTGCTCAGTGTATCGGACC.TTTTCTGGCCGCATGCAGC 8!-#8-8!-F!-8#!8-!88-##8-FF#FFFFFF!!F-F-F-FF!F--8-8-8#!!!!!88-!F-F-!#8---88!FF8-FF-#-!8-!88-8!#!8--F-FF8FF88F!F8F8!!8!-F!88-!!-F8!F#!8---!-!F!--8--!F!8 BC:Z:GTGGCAGA-GAAACGAA RG:Z:HiMom.1 +HiMom:1:1102:1127:1000 141 * 0 0 * * 0 0 CGCCGCTATTCCGGACA.AT.GTGTGACGCTTTCCGTCTCCCGTCGTCTCGATTTGGCGCC.ATC.TCCGTCAGCCTAGAG.A.TAACGAA.CTGGATGCTGC.CATTGGA.ATGACTACCTGCTACTTGG.ACGATTCTGCACGTCGTCT !88F8FFF!8888!-8-#F8#-8!!F-!FFF!888--8FF-F-F--8-!FF8-F888-F!8#F--#!88!!-F-FF!F-8-#-#!--FFF-#8-8-8-!-!-!#88F!!8F#F!8FFF8-F---FF!-888#F8FF8------88--8F!- BC:Z:GTGGCAGA-GAAACGAA RG:Z:HiMom.1 +HiMom:1:1102:1163:1000 77 * 0 0 * * 0 0 GATACGGTGTTATTCTTCTTGATTTGACTACG.GTCCGACAAC.TATTCGTGGAAACACGGCCCAATAGCGCT.GCCC.ACAGCTTTATAGTGTCA.CAGTGATTACGTCG.TGTCAGGGTTTACAATG.AG.GCAAGCGTTTGGCGGCGA !-!888F-8!!8!8--88!888---!8FF88F#--!F8-!-F8#F88F!88!!F-8F8-8!--!-F!FF!8-F#F!!8#-!F88F-!-FF!8FFFF#F-88F8F!8!!8FF#!8-!F888F8F--FF8-#88#-!--F88F!-F-!--!F- BC:Z:CCGCGCNC-NGGGATAT RG:Z:HiMom.1 +HiMom:1:1102:1163:1000 141 * 0 0 * * 0 0 CCTGCTCCTCGGCCGACCTG.CCCTAATGCAGTTGCTCCGGA.CTGCCAACGAAAACCTTACTC.TCTA.CTCGTA.ACTACGGCACTGAAGCA.TC.GCCC.TTTGTTC.CGTCTAACCACTCTTTCTTCGCGCGAT.TAAGGCCT.CTC F!-!-F88FF-!F-88F!-!#-8!8-F!88--8F!!FF--8F#-FF88FF---F8F8!88F8!-#F!!8#88!-FF#-!FF8!F-F!88F----#!-#-!F-#8!--!!8#88FFF88F8-8!!-!F888!!FF!8F8#8-F!!!-8#F!- BC:Z:CCGCGCNC-NGGGATAT RG:Z:HiMom.1 +HiMom:1:1102:1181:1000 77 * 0 0 * * 0 0 TAGCATCGTAAACGGGACTTCGCTAGTCCAGTCTCTTACTAGTCCGG.T.TGGACTA..GTT.TGTA.ACCCGACTCGGA.T.CATTAGTCAC.CAGACT.CTGT.G.CATCAA.GACCC.AC.CCTCCTTCCCAGATAACCGTT.GTTTC -F!!8F!F!F--!F-F--F!-!---8F!!F-FF-!F8F8F--F--8-#-#-8!F!!F##-88#-8F8#-!-8F--!-!!8#8#8-!F88-8--#-F--!-#!---#-#F-8FFF#8888F#8!#F-888!!!-FF-F!FFF!!!F#8!F88 BC:Z:CGCGTAGT-ATTCCGAC RG:Z:HiMom.1 +HiMom:1:1102:1181:1000 141 * 0 0 * * 0 0 GACT.AGCGATAACGTGGTTCTACGGC.C.GTATC.CTTACGTGGG.TTCTCAG.CGTGCGAGCCCGTGGCCCTGTGCCTCT.TCC.TCGCTGTTGGGTCCCTCACTATGGTTCGCGTTCTGCAGAGTGTG.GAGTTAACTC.C.GACGTG !8-8#-!!!F!888!!8F!!F!F!-FF#F#--FF!#!-888-8!8F#-FF!---#---F8-8!-88FFF8-F-8!F!!88!!#FF!#8!!-8FFF-F--F!!8--8FF!!---F888!-!F!8-F8!88!8#F-F8-8-F--#!#8888!F BC:Z:CGCGTAGT-ATTCCGAC RG:Z:HiMom.1 +HiMom:1:1102:1199:1000 77 * 0 0 * * 0 0 CTAGCTGTTGCGGCGTTCACGGTGTCGTGG.CTTGGACCACGCCATCCCTC.AG..CCTATAGTGA.CTCAAATGGTGGTCAATAACTCAGGTTGCTGCGCTCC.TC.TGCAATCCCTG.AAACCACCG.TGGGCCCGGCAGTAGAGCT.. 8F8!F-8F-8!!!8-!-8-!!!!F-!!8!-#8!!!-FFF888!--!-8F!8#F-##!!8F8-8!--#8!!-F-!88!!F!!8FF---!F88-!8--!!!-8F!8#88#!-F-8-F8F!!#--F8F8!8-#-8!F!!-F88F-8F-F!-F## BC:Z:TAACGGGT-GTGCACCG RG:Z:HiMom.1 +HiMom:1:1102:1199:1000 141 * 0 0 * * 0 0 TGTGATCTCACAGT.TCGATTA.TTCGGTGGCT.ATAGATATCGCGTGG.GTCCGGGTCGCCGCATCGG.CTTCAGC.AAGTT.GTCGTTTT.GCGAATAGCAACGCGGTGGGAA.AACGTTG.G.GATGGTTGGCGGT.TTTTAGTGCTT !8----8F-8F---#--8F-8-#8!8-!8!F-F#8-F!F!FF--F-F88#!FFF-8F!-8F--!-88!!#88-!888#---!8#!!!!8F!8#F-!-FF-!-F---F8!-!-8F-#F8-F-!F#!#8F-8-8F-F!--!#FF88F8-F!FF BC:Z:TAACGGGT-GTGCACCG RG:Z:HiMom.1 +HiMom:1:1102:1217:1000 77 * 0 0 * * 0 0 GGA.TCCCCGTT.CAGTTCCTCT.CGCCAACGACTATCAACAGCGCGTACATTGGGCTGTGCCCTTCAGTGGGTTA.GGCTTCGT.CGAAGTTCGGTTATGTCGTTTG.CCT.CCCATG.ACTAATTCTATCTCCCATG.TATTGCTCCCG 8F-#F--8!!!F#!88FF-8F8F#-FF8F8-!-!-F!-F-8-FF8F-8F!--8---F-8!!FF!F!F8-F-F-!!8#-FF!F8F!#8!---!-F-8-!F!F-F!!!!!#F8!#8!-F!8#8F!-F-8--F!-8!!-F-!#F8F--F8!FF! BC:Z:CTATCTGN-TTTGAGTA RG:Z:HiMom.1 +HiMom:1:1102:1217:1000 141 * 0 0 * * 0 0 ATGCGTTT.GTGCATA.AGGGGTCCAGTCTTCACTTGTTGAC.A.GCGAACCACA..TCGCCGTTTGGCA.CGTCAGGTCTTGGGAGTTCGGTCGCGTCATGTTGCG.GTGACCAGGCCCCTCGACTGCCTACTTCGCTTATCGGGCGGT. FF888F88#---F-!8#F88!8!FF8F8F!8F8!FFF!!-FF#8#--!FF8--!8##!8F8!!F!-FF-8#F-8--8!8!8F8-F8FF-8!88!8-F!88-FF8FF8#8F!F-F8!---8!F-!8!!F8888F!FF8F8--FF!--F-!8# BC:Z:CTATCTGN-TTTGAGTA RG:Z:HiMom.1 +HiMom:1:1102:1235:1000 77 * 0 0 * * 0 0 TCTC.CTATCGTT.AA.TATCACCTAGTTGGT.G.GGTGAAGTTGGATCTTTCTCTTATACACGGCAGACGTGCCGCTGAGGA.TTCGCC.AGTAAGCGATCTTGGTTGCTCCAGAGTTGCGTGA.TCGCTTAAAA.GCGCGGCTGTCACA F!-!#!FF-F8!8#88#!FFF8-F-F!FF-!F#!#!F!-F--8!8!-!FFF-8-FF!--8F-!--FF-F8F8-!-F-F8-F!8#!F!888#8!!-888!-!-!FF!-8!!!8F88-!!--F-!!F#!F!88-88-8#FFF--!F8-F-8-F BC:Z:CCGGTGCN-AAGTTACG RG:Z:HiMom.1 +HiMom:1:1102:1235:1000 141 * 0 0 * * 0 0 TCATAATGGGACT.ACGGGCTAAGTTC.GCGGCGT.ACGG.CTAAATGGGGCAC.CCCCGTCTACTCTTGCTCATATGCTTTAAA.GGGGCGATTTC.GCTTGCGGGATGCGGACGTCCCATGTTTTCA.GGGCCGCCCTAGTCCT..GGT !-F-8F-F!!8F8#-8-F!!!-8--!-#FFF--88#8!!F#-8-FF-8!-!8F8#88F8!8-F----8F-FF!F8-!8-8F8-F-#!8-88-F!F8!#88!!8F8---!!8-FF-!888-F-F-8-8-F#8!!-!F!!8-8F8-8!##-8- BC:Z:CCGGTGCN-AAGTTACG RG:Z:HiMom.1 +HiMom:1:1102:1253:1000 77 * 0 0 * * 0 0 CCTTCACACGTGAC.T.TATCATTCTGTTCTTGTATTTGGATTGCCCTCA.C.ATAT.GGCATCCTAAGCCCGGT.TGGTA.TATGCCTCTCCTCGATCCCGACA.GGTAACGTCCAAGGGA.GGTCAGCT.ACGAGATGGAGTTCAGGTC F8!F!-F88F8-8!#-#F8F!-F!!8!F!!-!F!-8--8FF-!8F-F!-8#!#--FF#8FFF-F--F8!-FFF-8#!8-FF#FF!F-8--!888!----!F8F88#F!8F8-!!!-8-F-!-#F-----!8#--8-!FF88FF-8F--!F! BC:Z:GANGCTGA-CCCGGCAT RG:Z:HiMom.1 +HiMom:1:1102:1253:1000 141 * 0 0 * * 0 0 GGCGCCCT.CTGTCATCCGTATGTG.TCGCTTGATTTA.CCGCC.ATATGGTGGCTCATCTCGCTCGGGGACCATGCCTATTAAG.GGG.AGTCTGTGGTT.AGTGCTCTTGA.CGATTCGCCTTCCC..AAAAGGTCTGACGTGCCGCGA -!F--!FF#F-!!FF--8FF8F--F#F-FF!8F88FFF#-FF8-#-F88---!8F8-8-8F-!-FF8!-F88!FF8-!F-8F88!#--F#--!-888F-FF#-!8!88-!!88#8FF8-8!8F!!8!-##8FF8F!!-F!F!-8FF-!8!8 BC:Z:GANGCTGA-CCCGGCAT RG:Z:HiMom.1 +HiMom:1:1102:1271:1000 77 * 0 0 * * 0 0 GCCAATTCCCAAAGTGTCGCTCCTTTGCGCTTA.TATGCGGTCCTCTACGTTACT.GGGCCATGG.GGGAACAT.TTC.CAGTCTACATTG..GGG.GTGCGGCTTT.CT..CCTGTTCT..GTCTCTA.TGGT.G.CTCCATCCCGGCAC !F-F8FF!-!8-88-!--F-8F-F8F8!FF!!-#FF!F88F8-8--FF8--!8FF#!!8FFFFFF#8F8-88F8#!8!#--F8!!F!-F-8##!8-#8-8F-8!!-!#F8##-F-!!-8F##--F-!-F#!FF8#-#8!F--888-8F-FF BC:Z:CCCAAGAA-AATCTGTG RG:Z:HiMom.1 +HiMom:1:1102:1271:1000 141 * 0 0 * * 0 0 G.GCCGTCTTTAATGTC.T.G.ACCTTATAATTCCGG.GCACGGATAG.GCGACTGCCCGCCGCG.CTTTCCGAGCTTTT.TAGTCGGTGTCTGTACATC.GCCCGGCATCTTGCTTCCGACATCGTC.GGGGGC.AGTATTGCAGACATA 8#!!8!8F-!!88-8-F#F#F#FF8!-F8FFF-FF8!#-FF!--8F-!#F8!88F8!-FFFF88F#F!FF--F-F-FF-F#!8-8!F8!8--8FFFF-F-#F!8FF!88!!-8!-8!!F88F8!F-8!#!8!F88#--F8FF!8FF-F88F BC:Z:CCCAAGAA-AATCTGTG RG:Z:HiMom.1 +HiMom:1:1102:1289:1000 77 * 0 0 * * 0 0 GCGTCTCAACATAT.ATTTATTCATATATGA.TTAAC.CAATCAGGAAACACCGGGACTTATCCGT.GGGTGCT..TGTCCTCGTCTTGGTGCGCTCAT.CTCTTTCCAGGTTTTAACGAGCGGACTCGATCCACTCTACATGGTACTTTT !-!8!!8FF----8#F-F8FFF8FFFF888-#!8F8-#!88!FF-888---8!8----888-!F8-#!-F!!8F##F8!-8!8F8F8-8-8F-8F!-8F#F8-!!----!-8FF!8FF!-FFF88-!-F-F-!8!-F8F!8F!-!-88!FF BC:Z:CGCTGCAC-CCGTNCAA RG:Z:HiMom.1 +HiMom:1:1102:1289:1000 141 * 0 0 * * 0 0 TTAGCAGCACA.CACGGCTTGTTGCGACTGGTCGTCT.ACCGTTCTAGTA.GA.GCCGGTGTCTAGGCCCCAA.GTGTCGCAACGGACCCCGGTCCCGCG.CC.CACCGA.CATG.TACTCG.ATCT.GATAAGGTCCAAATTGCTTCT.G !88!--8--!F#-8!-!----8F-F8F8!8!!8FF-8#88!-88-8F!!F#F-#8!FF88!F-!-!88!!8--#!8-F8F!-FF-F-8FF-!-F8FF88!#--#!-8!-F#--8!#F8FF88#-8!F#F-!-8F!88F88F!--!8FF!#! BC:Z:CGCTGCAC-CCGTNCAA RG:Z:HiMom.1 +HiMom:1:1102:1307:1000 77 * 0 0 * * 0 0 ATCCGCATTTAGATCACTTTTCC.TCCCCATGCGATCATTGATGCCTC.GAAGTTACTGCCAAGTACCGCG..CTCTGTCTTCCTTGGGGTTATTGGATGGGCTCCCCTGAAGGACATTTAAACACAGGATGAGCGATCCCTTCT.GTCAG -!!!88-8-!888F8F!!!8!-F#------8!!-F8---!8-----!!#8-FFFF8-!8-88F!8-8-!-F##F!-F8!8!FF-88!888FF-F8-FF8F!8F-FF-!8FF-8-8-F-88--F88--F----8FF8F8!8F8-!8#-88F8 BC:Z:TCGGTCTT-CCGACTGG RG:Z:HiMom.1 +HiMom:1:1102:1307:1000 141 * 0 0 * * 0 0 CGAGGATAGTA.ATCTTTTCA.G.TGCCTGGCAGTATCAGTCAAACTTGAACGGGTACGGGGAGAGGCTGTCCTGGGTG.AAGACCATTCTCCAC.GCGAATGACTAGAGTTGCCCATGATGGA.TATG.T..GACGAA.GTGCGTGCAT. !-F-F8!8!--#--88F---F#!#F!FFF8!FF88-8F-F!----FFF!F8-FF--F-F-F!F!F8FF-F!F-F!!FFF#---88F8!-!F-!88#F-FF--8F-F-8F8FFF-FF8!8----8#!F88#!##!8FFF-#!!88!8F!F-# BC:Z:TCGGTCTT-CCGACTGG RG:Z:HiMom.1 +HiMom:1:1102:1344:1000 77 * 0 0 * * 0 0 CTAGTGCAGG..TGCAATCGTTGTGTCA.GTGTTCTCGGAGAGAGATTCCGG.TCTTAGTTTTAT.GGGTTGGTCTAC.GCG.GTT.TCGTTTTTTAAGATTAGGC.CCGAATGC.CGAAG.AAAATGATGTCTGGCATTGTCTTCT.CG. !--!F8!88-##F---F-F!!!!88!-F#!!FFF--F-!FFFF--F-F!!!-#8!F-F-!!8!F!#!8F8!8-8F-F-#--F#8-8#!!-!-!FF-8---8-F8--#8!88--!F#!-F8F#F88FFFFFF!-!8!F-!F!8-!-!!#-F# BC:Z:CCAGTCAC-GGACCAGT RG:Z:HiMom.1 +HiMom:1:1102:1344:1000 141 * 0 0 * * 0 0 CCCGTGCT..TCTTACG.GTACGT.C..TATAGTCACG.AG.GAGTAAAC.CAAGT.CCGGCCGCCTCCAATATTCCTTTGATTTATC.AGGG.GAC.GCATC.GTCAATGTCA.CAACATA.ATCCTGTTAAGT.GGCTAG.GCACTCAA !8!-8!F-##8!8!FF8#!-FF!F#-##-8-F!F8--!#8!#!FFF8--8#-F8-!#-F!-F!F88!F!F-FF-88-F--88FF-8F-#--!F#!--#8-8F8#88F8FF!-F8#!-8F88-#8!F8F!88F88-#F!8!-!#F8-!88F8 BC:Z:CCAGTCAC-GGACCAGT RG:Z:HiMom.1 +HiMom:1:1102:1362:1000 77 * 0 0 * * 0 0 AGGG.CACTTTCGATTGATG.AATTCCATCCTATATCGATATTATTGTGTCCGCCTCAACTG.TGTCGCAGAATGCGCAATGAC.CCACC.ATGCAAGCTAGACGCGTGCGTCTTCGTGAGGT.AACTTACGATCGCTGGCCATATTGAAA 8--F#8F88-FFF-8!!8FF#-FF-!-88FF-8FFFF!-FF--8F!F!--!F8-8FF-F-8!#8!8F!88FFFF!F-F-F8!F!#-8-8-#--8!-F88F-FF88F!FF!8!-!!!8F8F8-F#8F-F8F--FF!888-88!-!F-F8-F8 BC:Z:CAACCTAT-ACGCTGNT RG:Z:HiMom.1 +HiMom:1:1102:1362:1000 141 * 0 0 * * 0 0 GACGTGCTGCTGCGTCCGTAGG.GC.CCTATACACAGGA.CTGTGGGATGGTTCAAAACTGTCAC..CG.GGATCTCGGGC.GTGCCTCGGAGTCAGCCTCTTT.GATGGTGAGAGAGGTCTGGTA.ACGAGGTTTCTAATGTTGGTCATT -F-F8F-8-8--F!8!-8!F!8#8F#8---F-8FF8F8F#F8-8F!F-!--!8F8FF8F--FF-F##F8#FF88!FF!!--#FF88!!!F--8---!8888-!F#!-!F--!F8-F-F-!-!8--8#F--FF!F-F-!8-F8-F-!F--F! BC:Z:CAACCTAT-ACGCTGNT RG:Z:HiMom.1 +HiMom:1:1102:1380:1000 77 * 0 0 * * 0 0 ACTGAGTGGTATCGGACACCGA.GCGTTAG.GGGTACGGC.GTGTTT.TGACCAAAGTTTCATCTCATCAGACATCCGTTTGGGCTGC.GCTTTGGCGCCAT.GCATAGTGTCGGATCGACGTGTCACCCCCAATGCCTTGGTATTCG.TG 8F8!F8!8!F-8F8--!-8!-8#8!-88--#F-8-8!-!8#8-F!F!#888!8F8FFF8F!8-F!8F8!F--FFF88!!FF88-F8!8#F!F8!8-!F8-8F#!-888F-F88-F8!FFF-F-!88-F-F8-F8-!88FF8-F-!F88#!- BC:Z:GNGGTGTG-GCCGCGGT RG:Z:HiMom.1 +HiMom:1:1102:1380:1000 141 * 0 0 * * 0 0 TGAGGCCGGAGCCGCGCCTT.CATGG.CCGGTGATTATGAATGCCGCTGTTCCTT.TG.GTAACGGTGTGTAATTGACGCGCACACCCTGAGC.GGTAT.GGC.ATC.GGA.ACTCCAAGTAGACGCCGTTCCTC.GATCTA.ACG.GTAT F-F-88!-FF-!F!88-!!8#!88-F#!F--!F-!-FF8F8FF8!--8F-FFF!!#8!#8--F!FFFF!!!F888-8F-88F888F-!!--8-#-!F88#FFF#F!8#!-8#---!!8FF-F8FF-8-F!8----#F--F88#F!F#!88! BC:Z:GNGGTGTG-GCCGCGGT RG:Z:HiMom.1 +HiMom:1:1102:1398:1000 77 * 0 0 * * 0 0 .TCA.AGGGCTTCGGCGAGCC.GTG..CCATTTTCTGGGTAATCTCGATAGCGACCCGT.CGAGA.ATTTTATGATTGCGTTCGAAACTTAGTTATGGTGCA.AGGCT.AATGGGTCCTGACTGAGTTTAAA.GCGTTCAC.CCCTTAGTC #-F8#F-!!-!-!F-!!88!-#-8F##F8-F8-F-888F-8-!-!!88F---8-F!F!!#F-8F-#---8-F8!8--8!FF!8!FFFFFFFF-!F-88!F-F#FFF88#8-8F--!-!F!-8FF8---8---#!F8FF!8F#F--88F!!8 BC:Z:GGTGTTGT-CGATCAGC RG:Z:HiMom.1 +HiMom:1:1102:1398:1000 141 * 0 0 * * 0 0 GCTCGCTTA.CTAGAACTCCTTCCACAGTCCCCCCCGTGCCTCCACGCG.CCAAGC.TCCGGGGCGTTACATGCGCTCGCC.AGG.CTATATGCTCTCCCCG.CTT.TCTAAAGTAGTTTTCCGGGTCGAGTATTAATAAGAAGGTAAGT. !F-F-88!-#8F88F-!-F!FF--F-FF!8F-FF8!FFF!-!8-8!F!!#!--F8!#F-8-88!!F!--F8F-F-F8F88!#-8-#FF--F-!!-F-F!F-F#!8-#F8F8F8F!FF!-F--8F!!FF!-8!8-FFF!F-F8--8!-8--# BC:Z:GGTGTTGT-CGATCAGC RG:Z:HiMom.1 +HiMom:1:1102:1416:1000 77 * 0 0 * * 0 0 TGACTACTTAGTAACGG.G.CCGTGGCCGCTACTGCGCCGAGGTTTTTATGTTTG.CAACTGGAAGGAGGCAATAAACTAAGA.CGATTGGCCCG.TAGGC..CGCGTCGGAACAGTTTCTCGCAATCAAC.CGTCGGCC.ATTCAAGCTC !--88--FF-!!F-F-!#!#-88F-!-8F--8!-!8F!----FFF8!8F8FF!!-#FFF!-!88F-!FFFF8F!F-88!F8!-#-F8!8!8-F8-#!F!8F##!8-F!-FF-FFF!F-FF-F8!-F8FF8F#-8-F8--F#8F8!FF8!F- BC:Z:TTAGCGTG-GTGCCAAG RG:Z:HiMom.1 +HiMom:1:1102:1416:1000 141 * 0 0 * * 0 0 TCGGCACGACTACTAGTAGCAC.CCGCCTGGGTCAC.TAGCCTCAGTTGGCTCAAATTTGGCTGGAATGACTAATCATATTTTGTCCATACAATCGATCTTTGGGCCTCCC.CCCCAT.A.CCGCGGGGTACCTTGTGCCTCTCACTTGCC -8!FF8!!8F8F8F-!!F8-8F#FF88!8-!!!FF-#-F8FF8F-FF-F-8-!8FF88!8-88-88F!-F!F888888-!!F8F!!FFFFF---!FF!-!F88--8---!F#-!8FF!#F#!-8!--!FF-!!F88!8FF--!88F88F!! BC:Z:TTAGCGTG-GTGCCAAG RG:Z:HiMom.1 +HiMom:1:1102:1434:1000 77 * 0 0 * * 0 0 CGGGGACAGTGTCATTATCGCC.CCG.GCAGG.TTAAG.C.T.CCGG.GGGGGCAGTGCTATTCCGATGTCCCCG.AATAGTC.TGGGTCAGTACCCATGCCCCTTATA.AGC.ATAT.GTAG.CAGCGGCTTGCGGCTCAGCCCATTTTA -8-8---F!8!-8-!!FF8!!-#8!-#8F-F8#F--8F#-#8#FF8F#-8FFF8-!8-!-8FF!-!-88F88!-!#8F8F-FF#!!-F888-F-!-888!FF!8FF8F-#88!#888!#8FF8#!888!-88!!8--8!!-8-FF-88!8F BC:Z:TNNGAGAA-TTACGCGC RG:Z:HiMom.1 +HiMom:1:1102:1434:1000 141 * 0 0 * * 0 0 CCCTATTGCACTTAG.GCGTGGAATCGCGGGATT.CGGCCCCCG.CAGTCGGCTATGATTCGA.TCCATGCGTGCGTGTGTGCGTATCCCCACGTATAAGAGCGCGGACACTCCA.CTGGGAACCAATC.CA.TGAC.TAGCCGACAATAT -8F-F8!F-F8-888#F8FF!!F8F!-8!8!8F-#8F!--8F!F#-8!F!8!-F8-!8F-FF-#-8--8!!88-----F-8--!!888!-F8!-88-----!8!88!8-8-!!-F#!--8!8-!!8--F#!-#F!--#F-F!-!-!F-F88 BC:Z:TNNGAGAA-TTACGCGC RG:Z:HiMom.1 +HiMom:1:1102:1470:1000 77 * 0 0 * * 0 0 CAGACCGCGGCTCTGGATCACCTCCGACGGGTAGTGACA.CTACCT.AATCCGTCCAAGCAATGTGCAGTTCTTAATGACTTGGCTCGAGTAGTCCTGACCAA.GAACGGACGTTCTTCGA.GATAGGTGGGAG.TGGCTTCACGCTTTAC 8FF8-FFF!F-8--F-888-!!-!-8--8FFFF!!F8FF#!!F!!8#F8!8F8-8-8-F!--8-F!8----!F----8-8-F!!-F!F-!F-!!F-F!FFFFF#F--F----!!F-!!F--#88!F!F!8-F--#-F8-F-!-!!-!!!-F BC:Z:GGGCAAAT-CTGGTNNN RG:Z:HiMom.1 +HiMom:1:1102:1470:1000 141 * 0 0 * * 0 0 AAGCAA.GA.GACACCGGTGTCAGTGTTTTGG.ATCGCAGCTTT.GACCTGCTTCCT.AACTT.TCTGTTTCCGAAGTCACTTATT.TAAACGAGCTCTGGACTAGGCTCTGTACTCCCAATCTCGT..TCTCGGGTCAA.GAGCCTGGCC F8-888#!8#-8--F--!F--888!8F8!-F8#-F!!!--!F8-#--8--F-!8FFF#--F!-#!F-!!!F-8-FF8--F!-88!8#88-F-F-8F--!8!F!-8-F--!88FF!-8!--8-!88F!##-!8-!!FF8-F#8FF-!!!--- BC:Z:GGGCAAAT-CTGGTNNN RG:Z:HiMom.1 +HiMom:1:1102:1488:1000 77 * 0 0 * * 0 0 CGCTGTGCGTAACTTCCATGAATATCGAGGTGGATCTC.GTAGTGTTTG.AC.ATAGGTACAAACGTCCAACATGTCACGTCGAGAACGCCCCGATGTGCGCGAGAAGT.ATGAGCGTATGCAGGGCGTCAATTGCCCTTGAGAAGGTGGG FF--8F88!!-8-F8!-FF!88F-!F8F!F!!F--F88#!88-F-F--F#8-#8-8-8-8!F-88!8!!FF88!FF!-8FFF--8-8F8-FF8--8FFFFF-FFF8888#F8!F!888-F!--!88-8!---FFF-!!F!FF--8F88-!! BC:Z:CTCATACG-CTGNTCCC RG:Z:HiMom.1 +HiMom:1:1102:1488:1000 141 * 0 0 * * 0 0 TCCTGACGGATACTTGCATAGGAC.CACTAGGT.TTGTCTATCTTTCAACGACAGGGA.A.TGTAAGGTGTTGAGTGTTCTCATGGCGTTATGGGCTCTTTC.C.ATTGTAGAG.CGGTGCGC.AGGCTGATTGACCCCGCATTGGGAATC !-8F--!FF8888!F--8-88-88#888-8!-F#F!-8-F888!!F-F-F!F!F-8-F#F#!F-8--FF--!--FF-!F!!88F!8!8-8-!-!-!F8F888#F#F!!!---F8#-F-F-FFF#8--FF-88--F--888FFFF88-8F!F BC:Z:CTCATACG-CTGNTCCC RG:Z:HiMom.1 diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/sams/TTGCGGCCGGTTTAAC.sam b/testdata/picard/illumina/125T8B8B125T_cbcl/sams/TTGCGGCCGGTTTAAC.sam new file mode 100644 index 000000000..1a0cc579f --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/sams/TTGCGGCCGGTTTAAC.sam @@ -0,0 +1,4 @@ +@HD VN:1.5 SO:queryname +@RG ID:HiMom.1 SM:SA_TTGCGGCCGGTTTAAC LB:LN_TTGCGGCCGGTTTAAC PL:illumina PU:HiMom.1.TTGCGGCC-GGTTTAAC CN:BI +HiMom:1:1101:1036:1000 77 * 0 0 * * 0 0 GTTAGGAGAGACACCC.GAAGACT.C.CACACCCTAT.TAATCGGGTGCATGTCGAT.AA..CTCGCCTCTGGGG.TGGTACCTAT.CTTAGTTCTTGCTCC.TA.ACGGCGCGATTGG.C.T.CGTTAGAGACCCTG.CCTACGGGGCTC !F!--!F8-FF8-8F!#F8F8-F8#-#8-8FF!!FF!#-F--F8!!!F!F--8-FF!#8F##-FF!F88-8-8-8#FFF8-8!8-F#--F8-F--!!!-8F!#!F#F--!FFF8F-F!-#8#8#!F8!-!-FF8FF!8#!FF8--8F8-!8 RG:Z:HiMom.1 +HiMom:1:1101:1036:1000 141 * 0 0 * * 0 0 CTCCGACCTG.ATGGATATCGTTAGCGGGTCCTGGTGAGGGC.CTCTA.CGTAC.GCGGAGAGCGCCCTGGACAACCCATACATCCACAGCACGAGGCTTTATGT.CTGT.TCCCGGCTCTGCCATTTTTCCA.GA.GTCTTGGCCCGTCC F8!8!FF8!-#8F!FF-FF88-!8!F8----88FFF-8F-F8#-!!8-#-!F8F#-8!88!F-F-F!-F8!FF8F8--FF8F--!!F!F-!8-F-F8-!F8-8!-#FF-8#!888!-88!-F!F8F-!FF!8F#F8#F--8!-F--F!8!- RG:Z:HiMom.1 diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/sams/barcode_double.params b/testdata/picard/illumina/125T8B8B125T_cbcl/sams/barcode_double.params new file mode 100644 index 000000000..a66be292b --- /dev/null +++ b/testdata/picard/illumina/125T8B8B125T_cbcl/sams/barcode_double.params @@ -0,0 +1,6 @@ +BARCODE_1 BARCODE_2 SAMPLE_ALIAS LIBRARY_NAME +CCCCGCTT TTGCGTGT SA_CCCCGCTTTTGCGTGT LN_CCCCGCTTTTGCGTGT +TTGCGGCC GGTTTAAC SA_TTGCGGCCGGTTTAAC LN_TTGCGGCCGGTTTAAC +CACCTAGT ACTCGAGT SA_CACCTAGTACTCGAGT LN_CACCTAGTACTCGAGT +GCTATAGT CCAGCAGC SA_GCTATAGTCCAGCAGC LN_GCTATAGTCCAGCAGC +N N SA_N LN_N diff --git a/testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/NovaSeq/InterOp/C1.1/EmpiricalPhasingMetricsOut.bin b/testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/NovaSeq/InterOp/C1.1/EmpiricalPhasingMetricsOut.bin new file mode 100755 index 000000000..b052b4806 Binary files /dev/null and b/testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/NovaSeq/InterOp/C1.1/EmpiricalPhasingMetricsOut.bin differ diff --git a/testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/NovaSeq/InterOp/C10.1/EmpiricalPhasingMetricsOut.bin b/testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/NovaSeq/InterOp/C10.1/EmpiricalPhasingMetricsOut.bin 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a/testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/NovaSeq/InterOp/IndexMetricsOut.bin b/testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/NovaSeq/InterOp/IndexMetricsOut.bin new file mode 100755 index 000000000..9cbc6bfbd Binary files /dev/null and b/testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/NovaSeq/InterOp/IndexMetricsOut.bin differ diff --git a/testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/NovaSeq/NovaSeq.illumina_lane_metrics b/testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/NovaSeq/NovaSeq.illumina_lane_metrics new file mode 100644 index 000000000..b1f641e49 --- /dev/null +++ b/testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/NovaSeq/NovaSeq.illumina_lane_metrics @@ -0,0 +1,7 @@ + +## METRICS CLASS picard.illumina.IlluminaLaneMetrics +CLUSTER_DENSITY LANE +1.38181 1 +1.38181 2 + + diff --git a/testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/NovaSeq/NovaSeq.illumina_phasing_metrics b/testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/NovaSeq/NovaSeq.illumina_phasing_metrics new file mode 100644 index 000000000..094a6682e --- /dev/null +++ b/testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/NovaSeq/NovaSeq.illumina_phasing_metrics @@ -0,0 +1,9 @@ + +## METRICS CLASS picard.illumina.IlluminaPhasingMetrics +LANE TYPE_NAME PHASING_APPLIED PREPHASING_APPLIED +1 FIRST 0.120793 0.077079 +1 SECOND 0.152156 0.084203 +2 FIRST 0.11915 0.075621 +2 SECOND 0.154134 0.085365 + + diff --git a/testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/NovaSeq/RunInfo.xml b/testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/NovaSeq/RunInfo.xml new file mode 100755 index 000000000..7f6274421 --- /dev/null +++ b/testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/NovaSeq/RunInfo.xml @@ -0,0 +1,11 @@ + + + + + + + + + + + diff --git a/testdata/picard/illumina/readerTests/C99.1.cbcl b/testdata/picard/illumina/readerTests/cbcls/C1.1/L001_1.cbcl similarity index 100% rename from testdata/picard/illumina/readerTests/C99.1.cbcl rename to testdata/picard/illumina/readerTests/cbcls/C1.1/L001_1.cbcl diff --git a/testdata/picard/illumina/readerTests/C100.1.cbcl b/testdata/picard/illumina/readerTests/cbcls/C2.1/L001_1.cbcl similarity index 100% rename from testdata/picard/illumina/readerTests/C100.1.cbcl rename to testdata/picard/illumina/readerTests/cbcls/C2.1/L001_1.cbcl diff --git a/testdata/picard/illumina/readerTests/cbcls/tile_1101.filter b/testdata/picard/illumina/readerTests/cbcls/tile_1101.filter new file mode 100644 index 000000000..445bc582e Binary files /dev/null and b/testdata/picard/illumina/readerTests/cbcls/tile_1101.filter differ