From be5e1148da6427184cbce11554d83f3e0f0f3673 Mon Sep 17 00:00:00 2001 From: jacarey Date: Tue, 20 Jun 2017 16:40:27 -0400 Subject: [PATCH 1/6] Added necessary plumbing to get new converter working with ExtractIlluminaBarcodes and CollectIlluminaBasecallingMetrics. --- .../java/picard/illumina/BasecallsConverter.java | 2 +- .../picard/illumina/CheckIlluminaDirectory.java | 4 +- .../CollectIlluminaBasecallingMetrics.java | 155 ++++++++++++----- .../picard/illumina/ExtractIlluminaBarcodes.java | 188 +++++++++++++++++---- .../picard/illumina/IlluminaBasecallsToFastq.java | 26 +-- .../picard/illumina/IlluminaBasecallsToSam.java | 26 +-- .../illumina/NewIlluminaBasecallsConverter.java | 125 +++----------- .../parser/IlluminaDataProviderFactory.java | 39 +++-- .../illumina/parser/NewIlluminaDataProvider.java | 60 ++----- .../picard/illumina/parser/readers/CbclReader.java | 28 +-- .../util/ThreadPoolExecutorWithExceptions.java | 37 ++++ .../illumina/IlluminaBasecallsToFastqTest.java | 3 +- .../illumina/parser/readers/CbclReaderTest.java | 9 +- .../Intensities/BaseCalls/s_1_1101_barcode.txt.gz | Bin 0 -> 358 bytes .../Intensities/BaseCalls/s_1_1102_barcode.txt.gz | Bin 0 -> 363 bytes 15 files changed, 403 insertions(+), 299 deletions(-) create mode 100644 src/main/java/picard/util/ThreadPoolExecutorWithExceptions.java create mode 100644 testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/s_1_1101_barcode.txt.gz create mode 100644 testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/s_1_1102_barcode.txt.gz diff --git a/src/main/java/picard/illumina/BasecallsConverter.java b/src/main/java/picard/illumina/BasecallsConverter.java index c1ccf9f04..b4abe6af6 100644 --- a/src/main/java/picard/illumina/BasecallsConverter.java +++ b/src/main/java/picard/illumina/BasecallsConverter.java @@ -133,7 +133,7 @@ void setTileLimits(Integer firstTile, Integer tileLimit) { /** * A comparator for tile numbers, which are not necessarily ordered by the number's value. */ - static final Comparator TILE_NUMBER_COMPARATOR = (integer1, integer2) -> { + public 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 diff --git a/src/main/java/picard/illumina/CheckIlluminaDirectory.java b/src/main/java/picard/illumina/CheckIlluminaDirectory.java index 068f9ee2e..4fc8fe262 100644 --- a/src/main/java/picard/illumina/CheckIlluminaDirectory.java +++ b/src/main/java/picard/illumina/CheckIlluminaDirectory.java @@ -167,7 +167,9 @@ protected int doWork() { filterFileMap.put(fileToTile(filterFile.getName()), filterFile); } - CbclReader reader = new CbclReader(cbcls, filterFileMap, readStructure.readLengths, tiles.get(0), locs, true); + OutputMapping outputMapping = new OutputMapping(readStructure); + + CbclReader reader = new CbclReader(cbcls, filterFileMap, readStructure.readLengths, tiles.get(0), locs, outputMapping.getOutputCycles(), true); reader.getAllTiles().forEach((key, value) -> { List fileForCycle = reader.getFilesForCycle(key); diff --git a/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java b/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java index 74e856626..f8930eaa5 100644 --- a/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java +++ b/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java @@ -38,26 +38,39 @@ import picard.illumina.parser.ClusterData; import picard.illumina.parser.IlluminaDataProviderFactory; import picard.illumina.parser.IlluminaDataType; +import picard.illumina.parser.IlluminaFileUtil; +import picard.illumina.parser.ParameterizedFileUtil; import picard.illumina.parser.ReadStructure; +import picard.illumina.parser.readers.AbstractIlluminaPositionFileReader; import picard.illumina.parser.readers.BclQualityEvaluationStrategy; +import picard.illumina.parser.readers.LocsFileReader; import picard.util.TabbedTextFileWithHeaderParser; import java.io.File; import java.text.DecimalFormat; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.HashMap; +import java.util.List; +import java.util.Map; import java.util.SortedMap; import java.util.TreeMap; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +import static picard.illumina.NewIlluminaBasecallsConverter.getTiledFiles; /*** - - * A Command line tool to collect Illumina Basecalling metrics for a sequencing run - - * Requires a Lane and an input file of Barcodes to expect. - - * Outputs metrics: - - * * Mean Clusters Per Tile - - * * Standard Deviation of Clusters Per Tile - - * * Mean Pf Clusters Per Tile - - * * Standard Deviation of Pf Clusters Per Tile - - * * Mean Percentage of Pf Clusters Per Tile - - * * Standard Deviation of Percentage of Pf Clusters Per Tile - - */ + - * A Command line tool to collect Illumina Basecalling metrics for a sequencing run + - * Requires a Lane and an input file of Barcodes to expect. + - * Outputs metrics: + - * * Mean Clusters Per Tile + - * * Standard Deviation of Clusters Per Tile + - * * Mean Pf Clusters Per Tile + - * * Standard Deviation of Pf Clusters Per Tile + - * * Mean Percentage of Pf Clusters Per Tile + - * * Standard Deviation of Percentage of Pf Clusters Per Tile + - */ @CommandLineProgramProperties( usage = CollectIlluminaBasecallingMetrics.USAGE_SUMMARY + CollectIlluminaBasecallingMetrics.USAGE_DETAILS, @@ -76,7 +89,7 @@ "

The input barcode_list.txt file is a file containing all of the sample and molecular barcodes and can be obtained from the " + "ExtractIlluminaBarcodes " + "tool.

" + - "" + + "" + "Note: Metrics labeled as percentages are actually expressed as fractions! " + "" + "

Usage example:

" + @@ -92,29 +105,31 @@ "definitions " + "for a complete description of the metrics produced by this tool.

" + - "
" - ; + "
"; //Command Line Arguments - @Option(doc="The Illumina basecalls output directory from which data are read", shortName="B") + @Option(doc = "The Illumina basecalls output directory from which data are read", 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; - @Option(doc="The lane whose data will be read", shortName = StandardOptionDefinitions.LANE_SHORT_NAME) + @Option(doc = "The lane whose data will be read", shortName = StandardOptionDefinitions.LANE_SHORT_NAME) public Integer LANE; // TODO: No longer optional after old workflows are through - @Option(doc="The file containing barcodes to expect from the run - barcodeData.#",shortName=StandardOptionDefinitions.INPUT_SHORT_NAME, optional = true) + @Option(doc = "The file containing barcodes to expect from the run - barcodeData.#", shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, optional = true) public File INPUT; - @Option(doc=ReadStructure.PARAMETER_DOC, shortName="RS") + @Option(doc = ReadStructure.PARAMETER_DOC, shortName = "RS") public String READ_STRUCTURE; - @Option(doc="The file to which the collected metrics are written", shortName= StandardOptionDefinitions.OUTPUT_SHORT_NAME, optional = true) + @Option(doc = "The file to which the collected metrics are written", shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, optional = true) public File OUTPUT; + @Option(doc = "Use the new converter", optional = true) + public boolean USE_NEW_CONVERTER = false; + private int barcodeLength = 0; private String unmatched_barcode; private final SortedMap barcodeToMetricCounts; @@ -159,9 +174,11 @@ protected int doWork() { barcodeToMetricCounts.put(barcode.toString(), new IlluminaMetricCounts(barcode.toString(), barcodeName, LANE)); } } - - factory = barcodeToMetricCounts.isEmpty() - ? new IlluminaDataProviderFactory( + if (USE_NEW_CONVERTER) { + factory = new IlluminaDataProviderFactory(BASECALLS_DIR, BARCODES_DIR, LANE, readStructure, bclQualityEvaluationStrategy); + } else { + factory = barcodeToMetricCounts.isEmpty() + ? new IlluminaDataProviderFactory( BASECALLS_DIR, BARCODES_DIR, LANE, @@ -169,7 +186,7 @@ protected int doWork() { bclQualityEvaluationStrategy, IlluminaDataType.PF, IlluminaDataType.Position) - : new IlluminaDataProviderFactory( + : new IlluminaDataProviderFactory( BASECALLS_DIR, BARCODES_DIR, LANE, @@ -178,18 +195,74 @@ protected int doWork() { IlluminaDataType.PF, IlluminaDataType.Position, IlluminaDataType.Barcodes); + } } unmatched_barcode = StringUtil.repeatCharNTimes('N', barcodeLength); //Initialize data provider, iterate over clusters, and collect statistics - final BaseIlluminaDataProvider provider = factory.makeDataProvider(); + // BaseIlluminaDataProvider provider; + if (USE_NEW_CONVERTER) { + File laneDir = new File(BASECALLS_DIR, IlluminaFileUtil.longLaneStr(LANE)); + + File[] cycleDirs = IOUtil.getFilesMatchingRegexp(laneDir, IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN); + + //CBCLs + List 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 + List locs = new ArrayList<>(); + File locsFile = new File(BASECALLS_DIR.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))); + File[] filterFiles = getTiledFiles(laneDir, laneTileRegex); + + IOUtil.assertFilesAreReadable(Arrays.asList(filterFiles)); + Pattern barcodeRegex = Pattern.compile(ParameterizedFileUtil.escapePeriods( + ParameterizedFileUtil.makeLaneTileRegex("_barcode.txt", LANE))); + Map barcodesFiles = new HashMap<>(); + for (File barcodeFile : getTiledFiles(laneDir, barcodeRegex)) { + Matcher tileMatcher = barcodeRegex.matcher(barcodeFile.getName()); + if (tileMatcher.matches()) { + barcodesFiles.put(Integer.valueOf(tileMatcher.group(1)), barcodeFile); + } + } - while (provider.hasNext()) { - final ClusterData cluster = provider.next(); - addCluster(cluster); + factory.getAvailableTiles().forEach(tile -> { + File barcodeFile = barcodesFiles.get(tile); + BaseIlluminaDataProvider provider = factory.makeDataProvider(cbcls, locs, filterFiles, tile, barcodeFile); + while (provider.hasNext()) { + addCluster(provider.next()); + } + }); + } else { + BaseIlluminaDataProvider provider = factory.makeDataProvider(); + + while (provider.hasNext()) { + final ClusterData cluster = provider.next(); + addCluster(cluster); + } } + onComplete(); return 0; } @@ -197,19 +270,19 @@ protected int doWork() { /*** * Process new cluster of Illumina data - increment a running counter of data */ - private void addCluster(final ClusterData cluster) { + private synchronized void addCluster(final ClusterData cluster) { //compute hash of Barcode and Lane for key String barcode = cluster.getMatchedBarcode(); if (barcode == null) barcode = unmatched_barcode; //increment counts - IlluminaMetricCounts counters = barcodeToMetricCounts.get(barcode); + IlluminaMetricCounts counters = barcodeToMetricCounts.get(barcode); if (counters == null) { - counters = new IlluminaMetricCounts(barcode,null,LANE); - barcodeToMetricCounts.put(barcode, counters); + counters = new IlluminaMetricCounts(barcode, null, LANE); + barcodeToMetricCounts.put(barcode, counters); } final int tileNumber = cluster.getTile(); - counters.incrementClusterCount(tileNumber,cluster.isPf()); + counters.incrementClusterCount(tileNumber, cluster.isPf()); } /** @@ -224,7 +297,8 @@ private void onComplete() { counts.addMetricsToFile(file); allLaneCounts.addIlluminaMetricCounts(counts); } - if (! barcodeToMetricCounts.keySet().contains("")) allLaneCounts.addMetricsToFile(file); // detect non-indexed case + if (!barcodeToMetricCounts.keySet().contains("")) + allLaneCounts.addMetricsToFile(file); // detect non-indexed case file.write(OUTPUT); } catch (final Exception ex) { throw new PicardException("Error writing output file " + OUTPUT.getPath(), ex); @@ -257,7 +331,7 @@ public IlluminaMetricCounts(final String barcode, final String barcodeName, fina /* Increments cluster count by 1 for a given tile number */ public void incrementClusterCount(final int tileNumber, final boolean isPf) { - incrementClusterCount(tileNumber,1d, isPf); + incrementClusterCount(tileNumber, 1d, isPf); } /* Increments cluster count by an amount for a given tile number */ @@ -273,31 +347,32 @@ public void incrementClusterCount(final Integer tileNumber, final double increme /* Handles calculating final metrics and updating the metric object */ private void onComplete() { - final double meanClustersPerTile = tileToClusterHistogram.getMeanBinSize(); + final double meanClustersPerTile = tileToClusterHistogram.getMeanBinSize(); metrics.MEAN_CLUSTERS_PER_TILE = Math.round(meanClustersPerTile); metrics.SD_CLUSTERS_PER_TILE = Math.round(tileToClusterHistogram.getStandardDeviationBinSize(meanClustersPerTile)); - final double meanPfClustersPerTile = tileToPfClusterHistogram.getMeanBinSize(); + final double meanPfClustersPerTile = tileToPfClusterHistogram.getMeanBinSize(); metrics.MEAN_PF_CLUSTERS_PER_TILE = Math.round(meanPfClustersPerTile); metrics.SD_PF_CLUSTERS_PER_TILE = Math.round(tileToPfClusterHistogram.getStandardDeviationBinSize(meanPfClustersPerTile)); final DecimalFormat decFormat = new DecimalFormat("#.##"); final Histogram laneToPctPfClusterHistogram = tileToPfClusterHistogram.divideByHistogram(tileToClusterHistogram); final double meanPctPfClustersPerTile = laneToPctPfClusterHistogram.getMeanBinSize(); - metrics.MEAN_PCT_PF_CLUSTERS_PER_TILE = (Double.isNaN(meanPctPfClustersPerTile) ? 0 : Double.valueOf(decFormat.format(meanPctPfClustersPerTile * 100))); + metrics.MEAN_PCT_PF_CLUSTERS_PER_TILE = (Double.isNaN(meanPctPfClustersPerTile) ? 0 : Double.valueOf(decFormat.format(meanPctPfClustersPerTile * 100))); metrics.SD_PCT_PF_CLUSTERS_PER_TILE = Double.valueOf(decFormat.format(laneToPctPfClusterHistogram.getStandardDeviationBinSize(meanPctPfClustersPerTile) * 100)); metrics.TOTAL_CLUSTERS = (long) this.tileToClusterHistogram.getSumOfValues(); - metrics.PF_CLUSTERS = (long) this.tileToPfClusterHistogram.getSumOfValues(); - + metrics.PF_CLUSTERS = (long) this.tileToPfClusterHistogram.getSumOfValues(); + final ReadStructure readStructure = new ReadStructure(READ_STRUCTURE); int templateBaseCountPerCluster = 0; - for (int i = 0; i < readStructure.templates.length(); i++) templateBaseCountPerCluster += readStructure.templates.get(i).length; + for (int i = 0; i < readStructure.templates.length(); i++) + templateBaseCountPerCluster += readStructure.templates.get(i).length; metrics.TOTAL_READS = metrics.TOTAL_CLUSTERS * readStructure.templates.length(); metrics.PF_READS = metrics.PF_CLUSTERS * readStructure.templates.length(); metrics.TOTAL_BASES = metrics.TOTAL_CLUSTERS * templateBaseCountPerCluster; metrics.PF_BASES = metrics.PF_CLUSTERS * templateBaseCountPerCluster; - + } /* Computes final metric based on data counts and writes to output metric file */ diff --git a/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java b/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java index 0016bc277..f66ae1dd8 100644 --- a/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java +++ b/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java @@ -25,10 +25,12 @@ import htsjdk.samtools.metrics.MetricBase; import htsjdk.samtools.metrics.MetricsFile; +import htsjdk.samtools.util.CloserUtil; import htsjdk.samtools.util.IOUtil; import htsjdk.samtools.util.Log; import htsjdk.samtools.util.SequenceUtil; import htsjdk.samtools.util.StringUtil; +import picard.PicardException; import picard.cmdline.CommandLineProgram; import picard.cmdline.CommandLineProgramProperties; import picard.cmdline.Option; @@ -38,12 +40,17 @@ import picard.illumina.parser.ClusterData; import picard.illumina.parser.IlluminaDataProviderFactory; import picard.illumina.parser.IlluminaDataType; +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 picard.util.TabbedTextFileWithHeaderParser; +import picard.util.ThreadPoolExecutorWithExceptions; import java.io.BufferedWriter; import java.io.File; @@ -55,9 +62,11 @@ import java.util.List; import java.util.Map; import java.util.Set; -import java.util.concurrent.ExecutorService; -import java.util.concurrent.Executors; +import java.util.concurrent.ThreadPoolExecutor; import java.util.concurrent.TimeUnit; +import java.util.regex.Pattern; + +import static picard.illumina.NewIlluminaBasecallsConverter.getTiledFiles; /** * Determine the barcode for each read in an Illumina lane. @@ -174,6 +183,9 @@ "the number available on the machine less NUM_PROCESSORS.") public int NUM_PROCESSORS = 1; + @Option(doc = "Use the new converter", optional = true) + public boolean USE_NEW_CONVERTER = false; + private static final Log LOG = Log.getInstance(ExtractIlluminaBarcodes.class); /** @@ -223,23 +235,78 @@ protected int doWork() { } LOG.info("Processing with " + numProcessors + " PerTileBarcodeExtractor(s)."); - final ExecutorService pool = Executors.newFixedThreadPool(numProcessors); - - // TODO: This is terribly inefficient; we're opening a huge number of files via the extractor constructor and we never close them. - final List extractors = new ArrayList(factory.getAvailableTiles().size()); - for (final int tile : factory.getAvailableTiles()) { - final PerTileBarcodeExtractor extractor = new PerTileBarcodeExtractor( - tile, - getBarcodeFile(tile), - barcodeToMetrics, - noMatchMetric, - factory, - MINIMUM_BASE_QUALITY, - MAX_NO_CALLS, - MAX_MISMATCHES, - MIN_MISMATCH_DELTA - ); - extractors.add(extractor); + final ThreadPoolExecutor pool = new ThreadPoolExecutorWithExceptions(numProcessors); + + final List extractors = new ArrayList<>(factory.getAvailableTiles().size()); + + if (USE_NEW_CONVERTER) { + File laneDir = new File(BASECALLS_DIR, IlluminaFileUtil.longLaneStr(LANE)); + + File[] cycleDirs = IOUtil.getFilesMatchingRegexp(laneDir, IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN); + + //CBCLs + List 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 + List locs = new ArrayList<>(); + File locsFile = new File(BASECALLS_DIR.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))); + File[] filterFiles = getTiledFiles(laneDir, laneTileRegex); + + IOUtil.assertFilesAreReadable(Arrays.asList(filterFiles)); + + for (final int tile : factory.getAvailableTiles()) { + final PerTileBarcodeExtractor extractor = new PerTileBarcodeExtractor( + tile, + getBarcodeFile(tile), + barcodeToMetrics, + noMatchMetric, + factory, + MINIMUM_BASE_QUALITY, + MAX_NO_CALLS, + MAX_MISMATCHES, + MIN_MISMATCH_DELTA, + cbcls, + locs, + filterFiles + ); + extractors.add(extractor); + } + } else { + // TODO: This is terribly inefficient; we're opening a huge number of files via the extractor constructor and we never close them. + for (final int tile : factory.getAvailableTiles()) { + final PerTileBarcodeExtractor extractor = new PerTileBarcodeExtractor( + tile, + getBarcodeFile(tile), + barcodeToMetrics, + noMatchMetric, + factory, + MINIMUM_BASE_QUALITY, + MAX_NO_CALLS, + MAX_MISMATCHES, + MIN_MISMATCH_DELTA + ); + extractors.add(extractor); + } } try { for (final PerTileBarcodeExtractor extractor : extractors) { @@ -379,7 +446,11 @@ private File getBarcodeFile(final int tile) { final IlluminaDataType[] datatypes = (MINIMUM_BASE_QUALITY > 0) ? new IlluminaDataType[]{IlluminaDataType.BaseCalls, IlluminaDataType.PF, IlluminaDataType.QualityScores} : new IlluminaDataType[]{IlluminaDataType.BaseCalls, IlluminaDataType.PF}; - factory = new IlluminaDataProviderFactory(BASECALLS_DIR, LANE, readStructure, bclQualityEvaluationStrategy, datatypes); + if (USE_NEW_CONVERTER) { + factory = new IlluminaDataProviderFactory(BASECALLS_DIR, OUTPUT_DIR, LANE, readStructure, bclQualityEvaluationStrategy); + } else { + factory = new IlluminaDataProviderFactory(BASECALLS_DIR, LANE, readStructure, bclQualityEvaluationStrategy, datatypes); + } if (BARCODE_FILE != null) { parseBarcodeFile(messages); @@ -459,6 +530,8 @@ private void parseBarcodeFile(final ArrayList messages) { * do not match a barcode. */ public String BARCODE; + + public String BARCODE_WITHOUT_DELIMITER; /** * The barcode name. */ @@ -530,6 +603,7 @@ public BarcodeMetric(final String barcodeName, final String libraryName, final String barcodeDisplay, final String[] barcodeSeqs) { this.BARCODE = barcodeDisplay; + this.BARCODE_WITHOUT_DELIMITER = barcodeDisplay.replaceAll(IlluminaUtil.BARCODE_DELIMITER, ""); this.BARCODE_NAME = barcodeName; this.LIBRARY_NAME = libraryName; this.barcodeBytes = new byte[barcodeSeqs.length][]; @@ -551,6 +625,7 @@ public BarcodeMetric() { public static BarcodeMetric copy(final BarcodeMetric metric) { final BarcodeMetric result = new BarcodeMetric(); result.BARCODE = metric.BARCODE; + result.BARCODE_WITHOUT_DELIMITER = metric.BARCODE_WITHOUT_DELIMITER; result.BARCODE_NAME = metric.BARCODE_NAME; result.LIBRARY_NAME = metric.LIBRARY_NAME; result.barcodeBytes = metric.barcodeBytes; @@ -583,9 +658,45 @@ public void merge(final BarcodeMetric metric) { private final BarcodeMetric noMatch; private Exception exception = null; private final boolean usingQualityScores; - private final BaseIlluminaDataProvider provider; + private BaseIlluminaDataProvider provider = null; private final ReadStructure outputReadStructure; private final int maxNoCalls, maxMismatches, minMismatchDelta, minimumBaseQuality; + private List cbcls = null; + private List locs = null; + private File[] filterFiles = null; + private IlluminaDataProviderFactory factory = null; + + public PerTileBarcodeExtractor( + final int tile, + final File barcodeFile, + final Map barcodeToMetrics, + final BarcodeMetric noMatchMetric, + final IlluminaDataProviderFactory factory, + final int minimumBaseQuality, + final int maxNoCalls, + final int maxMismatches, + final int minMismatchDelta, + List cbcls, + List locs, + File[] filterFiles) { + this.tile = tile; + this.barcodeFile = barcodeFile; + this.usingQualityScores = minimumBaseQuality > 0; + this.maxNoCalls = maxNoCalls; + this.maxMismatches = maxMismatches; + this.minMismatchDelta = minMismatchDelta; + this.minimumBaseQuality = minimumBaseQuality; + this.metrics = new LinkedHashMap<>(barcodeToMetrics.size()); + for (final String key : barcodeToMetrics.keySet()) { + this.metrics.put(key, BarcodeMetric.copy(barcodeToMetrics.get(key))); + } + this.noMatch = BarcodeMetric.copy(noMatchMetric); + this.cbcls = cbcls; + this.locs = locs; + this.factory = factory; + this.filterFiles = filterFiles; + this.outputReadStructure = factory.getOutputReadStructure(); + } /** * Utility class to hang onto data about the best match for a given barcode @@ -659,6 +770,10 @@ public synchronized Exception getException() { */ synchronized public void run() { try { + //delayed instantiation for new provider + if (this.provider == null) { + this.provider = factory.makeDataProvider(cbcls, locs, filterFiles, tile, null); + } LOG.info("Extracting barcodes for tile " + tile); //Sometimes makeDataProvider takes a while waiting for slow file IO, for each tile the needed set of files @@ -674,6 +789,7 @@ synchronized public void run() { while (provider.hasNext()) { // Extract the barcode from the cluster and write it to the file for the tile final ClusterData cluster = provider.next(); + for (int i = 0; i < barcodeIndices.length; i++) { barcodeSubsequences[i] = cluster.getRead(barcodeIndices[i]).getBases(); if (usingQualityScores) qualityScores[i] = cluster.getRead(barcodeIndices[i]).getQualities(); @@ -697,7 +813,8 @@ synchronized public void run() { LOG.error(e, "Error processing tile ", this.tile); this.exception = e; } finally { - provider.close(); + CloserUtil.close(provider); + provider = null; } } @@ -753,10 +870,10 @@ public static BarcodeMatch findBestBarcodeAndUpdateMetrics(final byte[][] readSu // If we have something that's not a "match" but matches one barcode // slightly, we output that matching barcode in lower case - if (numNoCalls + numMismatchesInBestBarcode < totalBarcodeReadBases) { + if (numNoCalls + numMismatchesInBestBarcode < totalBarcodeReadBases && bestBarcodeMetric != null) { match.mismatches = numMismatchesInBestBarcode; match.mismatchesToSecondBest = numMismatchesInSecondBestBarcode; - match.barcode = bestBarcodeMetric.BARCODE.toLowerCase().replaceAll(IlluminaUtil.BARCODE_DELIMITER, ""); + match.barcode = bestBarcodeMetric.BARCODE_WITHOUT_DELIMITER.toLowerCase(); } else { match.mismatches = totalBarcodeReadBases; match.barcode = ""; @@ -780,7 +897,7 @@ public static BarcodeMatch findBestBarcodeAndUpdateMetrics(final byte[][] readSu } match.matched = true; - match.barcode = bestBarcodeMetric.BARCODE.replaceAll(IlluminaUtil.BARCODE_DELIMITER, ""); + match.barcode = bestBarcodeMetric.BARCODE_WITHOUT_DELIMITER; } else { ++noMatchBarcodeMetric.READS; if (passingFilter) { @@ -798,16 +915,25 @@ public static BarcodeMatch findBestBarcodeAndUpdateMetrics(final byte[][] readSu */ 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++) { - final int basesToCheck = Math.min(barcodeBytes[j].length, readSubsequence[j].length); - for (int i = 0; i < basesToCheck; ++i) { - if (!SequenceUtil.isNoCall(readSubsequence[j][i])) { - if (!SequenceUtil.basesEqual(barcodeBytes[j][i], readSubsequence[j][i])) ++numMismatches; - else if (qualities != null && qualities[j][i] < minimumBaseQuality) ++numMismatches; + for (int i = 0; i < barcodeBytes[j].length; ++i) { + if (readSubsequence[j].length <= i) { + break; + } + if (SequenceUtil.isNoCall(readSubsequence[j][i])) { + continue; + } + if (!SequenceUtil.basesEqual(barcodeBytes[j][i], readSubsequence[j][i])) { + ++numMismatches; + continue; + } + if (qualities != null && qualities[j][i] < minimumBaseQuality) { + ++numMismatches; } } } + return numMismatches; } } diff --git a/src/main/java/picard/illumina/IlluminaBasecallsToFastq.java b/src/main/java/picard/illumina/IlluminaBasecallsToFastq.java index da3df57df..ecc7f61f4 100644 --- a/src/main/java/picard/illumina/IlluminaBasecallsToFastq.java +++ b/src/main/java/picard/illumina/IlluminaBasecallsToFastq.java @@ -30,7 +30,6 @@ 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; @@ -45,7 +44,6 @@ 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; @@ -201,18 +199,6 @@ @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. */ @@ -287,14 +273,7 @@ private void initialize() { } final int readsPerCluster = readStructure.templates.length() + readStructure.sampleBarcodes.length(); 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."); - } - - final MetricsFile metricsFile = getMetricsFile(); - + if (BARCODES_DIR == null) BARCODES_DIR = BASECALLS_DIR; 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, @@ -302,8 +281,7 @@ private void initialize() { 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); + this.APPLY_EAMSS_FILTER, INCLUDE_NON_PF_READS, IGNORE_UNEXPECTED_BARCODES); } 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, diff --git a/src/main/java/picard/illumina/IlluminaBasecallsToSam.java b/src/main/java/picard/illumina/IlluminaBasecallsToSam.java index 577969bcd..2da8c2421 100644 --- a/src/main/java/picard/illumina/IlluminaBasecallsToSam.java +++ b/src/main/java/picard/illumina/IlluminaBasecallsToSam.java @@ -31,7 +31,6 @@ 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; @@ -44,7 +43,6 @@ import picard.cmdline.Option; 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; @@ -258,19 +256,6 @@ @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; private BasecallsConverter basecallsConverter; @@ -312,21 +297,14 @@ private void initialize() { } 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."); - } + if (BARCODES_DIR == null) BARCODES_DIR = BASECALLS_DIR; 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); + this.APPLY_EAMSS_FILTER, INCLUDE_NON_PF_READS, IGNORE_UNEXPECTED_BARCODES); } 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, diff --git a/src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java b/src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java index 708b710c0..673a09daa 100644 --- a/src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java +++ b/src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java @@ -1,26 +1,20 @@ 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 picard.util.ThreadPoolExecutorWithExceptions; import java.io.File; import java.util.ArrayList; @@ -30,10 +24,6 @@ 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; @@ -41,19 +31,12 @@ 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<>()); + private final Map barcodesFiles = new HashMap<>(); /** * @param basecallsDir Where to read basecalls from. @@ -74,12 +57,6 @@ * @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, @@ -94,33 +71,15 @@ public NewIlluminaBasecallsConverter(final File basecallsDir, File barcodesDir, 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) { + final boolean ignoreUnexpectedBarcodes) { 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)); }); @@ -151,11 +110,11 @@ public NewIlluminaBasecallsConverter(final File basecallsDir, File barcodesDir, IOUtil.assertFileIsReadable(locsFile); //filter - Pattern laneTileRegex = Pattern.compile(ParameterizedFileUtil.escapePeriods( + Pattern filterRegex = Pattern.compile(ParameterizedFileUtil.escapePeriods( ParameterizedFileUtil.makeLaneTileRegex(".filter", lane))); - filterFiles = getTiledFiles(laneDir, laneTileRegex); + filterFiles = getTiledFiles(laneDir, filterRegex); for (File filterFile : filterFiles) { - Matcher tileMatcher = laneTileRegex.matcher(filterFile.getName()); + Matcher tileMatcher = filterRegex.matcher(filterFile.getName()); if (tileMatcher.matches()) { tiles.add(Integer.valueOf(tileMatcher.group(1))); } @@ -163,20 +122,23 @@ public NewIlluminaBasecallsConverter(final File basecallsDir, File barcodesDir, 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); + if (demultiplex) { + Pattern barcodeRegex = Pattern.compile(ParameterizedFileUtil.escapePeriods( + ParameterizedFileUtil.makeLaneTileRegex("_barcode.txt(\\.gz|\\.bz2)?", lane))); + File[] barcodeTileFiles = getTiledFiles(barcodesDir, barcodeRegex); + if (barcodeTileFiles.length != tiles.size()) { + throw new PicardException("Barcode files are required for each tile."); + } + for (File barcodeFile : barcodeTileFiles) { + Matcher tileMatcher = barcodeRegex.matcher(barcodeFile.getName()); + if (tileMatcher.matches()) { + barcodesFiles.put(Integer.valueOf(tileMatcher.group(1)), barcodeFile); + } } } - this.noMatchMetric = new BarcodeMetric(null, null, IlluminaUtil.barcodeSeqsToString(noMatchBarcode), noMatchBarcode); - + this.factory.setApplyEamssFiltering(applyEamssFiltering); + setTileLimits(firstTile, tileLimit); } public static File[] getTiledFiles(File baseDirectory, Pattern pattern) { @@ -196,7 +158,7 @@ public void doTileProcessing() { ThreadPoolExecutor tileProcessingExecutor = new ThreadPoolExecutorWithExceptions(numThreads); for (Integer tile : tiles) { - tileProcessingExecutor.submit(new TileProcessor(tile)); + tileProcessingExecutor.submit(new TileProcessor(tile, barcodesFiles.get(tile))); } tileProcessingExecutor.shutdown(); @@ -206,17 +168,6 @@ public void doTileProcessing() { 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) { @@ -275,15 +226,16 @@ public void run() { private class TileProcessor implements Runnable { private final int tileNum; private final Map> barcodeToRecordCollection = new HashMap<>(); + private final File barcodeFile; - TileProcessor(int tileNum) { + TileProcessor(int tileNum, File barcodeFile) { this.tileNum = tileNum; + this.barcodeFile = barcodeFile; } @Override public void run() { - final BaseIlluminaDataProvider dataProvider = factory.makeDataProvider(cbcls, locs, filterFiles, tileNum, barcodesMetrics, - noMatchMetric, maxNoCalls, maxMismatches, minMismatchDelta, minimumBaseQuality); + final BaseIlluminaDataProvider dataProvider = factory.makeDataProvider(cbcls, locs, filterFiles, tileNum, barcodeFile); while (dataProvider.hasNext()) { final ClusterData cluster = dataProvider.next(); @@ -338,33 +290,6 @@ private synchronized void addRecord(final String barcode, final CLUSTER_OUTPUT_R } } - 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 { diff --git a/src/main/java/picard/illumina/parser/IlluminaDataProviderFactory.java b/src/main/java/picard/illumina/parser/IlluminaDataProviderFactory.java index 2b834c34f..057faa4f0 100644 --- a/src/main/java/picard/illumina/parser/IlluminaDataProviderFactory.java +++ b/src/main/java/picard/illumina/parser/IlluminaDataProviderFactory.java @@ -24,10 +24,11 @@ package picard.illumina.parser; +import htsjdk.samtools.util.IOUtil; import htsjdk.samtools.util.Log; import htsjdk.samtools.util.StringUtil; import picard.PicardException; -import picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric; +import picard.illumina.NewIlluminaBasecallsConverter; import picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat; import picard.illumina.parser.readers.AbstractIlluminaPositionFileReader; import picard.illumina.parser.readers.BclQualityEvaluationStrategy; @@ -44,9 +45,12 @@ import java.util.Set; import java.util.SortedSet; import java.util.TreeSet; +import java.util.regex.Matcher; +import java.util.regex.Pattern; import static htsjdk.samtools.util.CollectionUtil.makeList; import static htsjdk.samtools.util.CollectionUtil.makeSet; +import static picard.illumina.NewIlluminaBasecallsConverter.getTiledFiles; /** * IlluminaDataProviderFactory accepts options for parsing Illumina data files for a lane and creates an @@ -113,7 +117,7 @@ private final IlluminaFileUtil fileUtil; - private final List availableTiles; + private List availableTiles; private final OutputMapping outputMapping; private final BclQualityEvaluationStrategy bclQualityEvaluationStrategy; @@ -201,7 +205,25 @@ public IlluminaDataProviderFactory(File basecallDirectory, File barcodesDirector this.formatToDataTypes = null; this.availableTiles = null; this.fileUtil = null; + outputMapping = new OutputMapping(readStructure); + + Pattern laneTileRegex = Pattern.compile(ParameterizedFileUtil.escapePeriods( + ParameterizedFileUtil.makeLaneTileRegex(".filter", lane))); + File laneDir = new File(basecallDirectory, IlluminaFileUtil.longLaneStr(lane)); + + List tiles = new ArrayList<>(); + 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(NewIlluminaBasecallsConverter.TILE_NUMBER_COMPARATOR); + availableTiles = tiles; } /** @@ -235,21 +257,12 @@ public void setApplyEamssFiltering(final boolean applyEamssFiltering) { * * @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 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); + File[] filterFiles, int tileNum, File barcodeFile) { + return new NewIlluminaDataProvider(cbcls, locs, filterFiles, lane, tileNum, outputMapping, barcodeFile); } public BaseIlluminaDataProvider makeDataProvider() { diff --git a/src/main/java/picard/illumina/parser/NewIlluminaDataProvider.java b/src/main/java/picard/illumina/parser/NewIlluminaDataProvider.java index d7d7c41c3..ffe32e71a 100644 --- a/src/main/java/picard/illumina/parser/NewIlluminaDataProvider.java +++ b/src/main/java/picard/illumina/parser/NewIlluminaDataProvider.java @@ -1,8 +1,7 @@ package picard.illumina.parser; -import picard.illumina.ExtractIlluminaBarcodes; -import picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric; import picard.illumina.parser.readers.AbstractIlluminaPositionFileReader; +import picard.illumina.parser.readers.BarcodeFileReader; import picard.illumina.parser.readers.CbclReader; import java.io.File; @@ -12,58 +11,38 @@ 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; + private BarcodeFileReader barcodeReader = null; /** * 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) { + final File[] filterFiles, final int lane, final int tileNum, + final OutputMapping outputMapping, final File barcodeFile) { 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; + this.reader = new CbclReader(cbcls, filterFileMap, outputMapping.getOutputReadLengths(), tileNum, locs, outputMapping.getOutputCycles(), false); + if (barcodeFile != null) { + this.barcodeReader = new BarcodeFileReader(barcodeFile); + } } @Override public void close() { + reader.clear(); reader.close(); } @@ -86,25 +65,12 @@ public ClusterData next() { 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(); + if (barcodeReader != null) { + cluster.setMatchedBarcode(barcodeReader.next()); } + addReadData(cluster, numReads, cbclData); - final ExtractIlluminaBarcodes.PerTileBarcodeExtractor.BarcodeMatch match = findBestBarcodeAndUpdateMetrics(barcodeSubsequences, qualityScores, - true, barcodeMetricMap, noMatchMetric, maxNoCalls, maxMismatches, - minMismatchDelta, minimumBaseQuality); - - if (match.isMatched()) { - cluster.setMatchedBarcode(match.getBarcode()); - } return cluster; } diff --git a/src/main/java/picard/illumina/parser/readers/CbclReader.java b/src/main/java/picard/illumina/parser/readers/CbclReader.java index e8f1b94c9..490b1e2fb 100644 --- a/src/main/java/picard/illumina/parser/readers/CbclReader.java +++ b/src/main/java/picard/illumina/parser/readers/CbclReader.java @@ -65,25 +65,28 @@ public class CbclReader extends BaseBclReader implements CloseableIterator { - private final byte[][] cachedTile; + private byte[][] cachedTile; private final int[] cachedTilePosition; private CbclData queue = null; private Iterator positionInfoIterator; private final CycleData[] cycleData; private final Map filterFileMap; - private final Map cachedFilter = new HashMap<>(); + private final Map> cachedFilter = new HashMap<>(); private final Map> surfaceToTileToCbclMap; private int headerSize; private Map> allTiles = new HashMap<>(); + private final int[] outputCycles; 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$"); + private static final Pattern PATTERN = Pattern.compile("^.+C(\\d{1,4}).+L(\\d{1,3})_(\\d).cbcl$"); public CbclReader(final List cbcls, final Map filterFileMap, final int[] outputLengths, - int tileNum, List locs, boolean headerOnly) { + int tileNum, List locs, int[] outputCycles, boolean headerOnly) { super(outputLengths); + this.outputCycles = outputCycles; + surfaceToTileToCbclMap = sortCbcls(cbcls); this.filterFileMap = filterFileMap; cycleData = new CycleData[cycles]; @@ -110,7 +113,7 @@ private void readSurfaceTile(int tileNum, List= cachedTile[totalCycleCount].length) { + if (cachedTilePosition[totalCycleCount] >= cachedTile[totalCycleCount].length + || cachedTilePosition[totalCycleCount] >= cycleData[totalCycleCount].getTileInfo().getNumClustersInTile()) { // end of tile return; } @@ -286,13 +290,12 @@ private void advance() { } private void cacheFilterAndLocs(TileData currentTileData, List locs) { - boolean[] filterValues = new boolean[currentTileData.numClustersInTile]; + List filterValues = new ArrayList<>(); FilterFileReader reader = new FilterFileReader(filterFileMap.get(currentTileData.tileNum)); Iterator positionInfoIterator = locs.iterator(); - int count = 0; + while (reader.hasNext()) { - filterValues[count] = reader.next(); - count++; + filterValues.add(reader.next()); } List positions = new ArrayList<>(); @@ -361,7 +364,7 @@ private void cacheTile(int totalCycleCount, TileData tileData, CycleData current // Write buffer contents to cached tile array // if nonPF reads are included we need to strip them out if (!currentCycleData.pfExcluded) { - boolean[] filterDatas = cachedFilter.get(tileData.tileNum); + List filterDatas = cachedFilter.get(tileData.tileNum); int sum = 0; for (boolean b : filterDatas) { sum += b ? 1 : 0; @@ -406,4 +409,7 @@ public int getHeaderSize() { return allTiles; } + public void clear() { + cachedTile = null; + } } diff --git a/src/main/java/picard/util/ThreadPoolExecutorWithExceptions.java b/src/main/java/picard/util/ThreadPoolExecutorWithExceptions.java new file mode 100644 index 000000000..30f656b41 --- /dev/null +++ b/src/main/java/picard/util/ThreadPoolExecutorWithExceptions.java @@ -0,0 +1,37 @@ +package picard.util; + +import picard.PicardException; + +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; + +public class ThreadPoolExecutorWithExceptions extends ThreadPoolExecutor { + public 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); + } + } +} diff --git a/src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java b/src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java index 16184f5c8..67901e558 100644 --- a/src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java +++ b/src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java @@ -167,8 +167,7 @@ private void runNewConverterTest(final int lane, final String jobName, final Str "MACHINE_NAME=machine1", "FLOWCELL_BARCODE=abcdeACXX", "USE_NEW_CONVERTER=true", - "NUM_PROCESSORS=2", - "METRICS_FILE=" + new File(outputDir, "test.metrics") + "NUM_PROCESSORS=2" }); final ReadStructure readStructure = new ReadStructure(readStructureString); diff --git a/src/test/java/picard/illumina/parser/readers/CbclReaderTest.java b/src/test/java/picard/illumina/parser/readers/CbclReaderTest.java index 15529ea41..850a0ace3 100644 --- a/src/test/java/picard/illumina/parser/readers/CbclReaderTest.java +++ b/src/test/java/picard/illumina/parser/readers/CbclReaderTest.java @@ -13,8 +13,8 @@ public class CbclReaderTest { 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 PASSING_CBCL_C1_1 = new File(TestDataDir + "/C1.1", "L001_1.cbcl"); + public static final File PASSING_CBCL_C2_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 char[] expectedBases = new char[]{ @@ -31,9 +31,8 @@ public void testReadValidFile() { filters.put(1101, TILE_1101_FILTER); 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); + final CbclReader reader = new CbclReader(Arrays.asList(PASSING_CBCL_C1_1, PASSING_CBCL_C2_1), + filters, new int[]{2}, 1101, locs, new int[]{1, 2}, false); int i = 0; while (reader.hasNext()) { diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/s_1_1101_barcode.txt.gz b/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/s_1_1101_barcode.txt.gz new file mode 100644 index 0000000000000000000000000000000000000000..07d51a6127bd83aa5ce63318b123bcfd2060bb4b GIT binary patch literal 358 zcmV-s0h#_EiwFP!000000CiI_ZonW6oZ&H6Xon`F<-uDgFC7sBAK?G$ol|uQL5YaK zy7S#RZYJuXX5rk*cbQ}L)#niEA!)DhjT*%2o*&DGBuI$==7HoIci= z*r~hK><(B)5w}4P$dd*|3PA^eW5+v#S}Io-3cWxNVysN43D^nL-p9=iMzjVjllqe>t?1TrE+SQX7-K=tG3Kppx=aKZM_ z!kcRR49cOwEDB5QJr`IL88Im2Ek6ixBH9kvo1KplnjY@jjDiMjowVE-c<>MS|8b=3o8mTc z9tadtBxO}~b9FaU)6nuN^{lm@t)I2mhG*Hou(mJ{i9mI@YXmBLZ?(0GtM`7Mwd}XD z@0$=PEL0NLQQ3e<%v#UJH7gCQ!4ljfl6{GJ-$-nchq;eFaR9gHA02%j6Vk;k0Bk1V zD?vv&HmWd%a#aPtE}Ps*4M3b?;?%9NqW&q*jb))&Xc36EVtzo*7G#77oG?B8xd2Xo z(np8w;p%VFxz8pECx{b1Cg#P-^v9L%pgsO!L(K*9#x@yF+LJx3otzF4(GoHc{xX~) zD8sX95E59&c#xZ*G3PDHZ@GNB(Q`zIsDY~a`aum$r=6P3%ChpoxsZ{JXY7f1nTug0 z%dj}Spte=vcWMqDn}#C{M?Va?NDgEsXbHI Date: Tue, 27 Jun 2017 16:03:28 -0400 Subject: [PATCH 2/6] Initial review changes. --- .../picard/illumina/CheckIlluminaDirectory.java | 46 +++--- .../CollectIlluminaBasecallingMetrics.java | 155 +++++++++++---------- .../picard/illumina/ExtractIlluminaBarcodes.java | 68 +++++---- .../picard/illumina/IlluminaBasecallsToSam.java | 4 +- .../illumina/NewIlluminaBasecallsConverter.java | 62 ++++----- .../picard/illumina/parser/readers/CbclReader.java | 114 +++++++-------- .../util/ThreadPoolExecutorWithExceptions.java | 21 ++- 7 files changed, 241 insertions(+), 229 deletions(-) diff --git a/src/main/java/picard/illumina/CheckIlluminaDirectory.java b/src/main/java/picard/illumina/CheckIlluminaDirectory.java index 4fc8fe262..afd6d07b0 100644 --- a/src/main/java/picard/illumina/CheckIlluminaDirectory.java +++ b/src/main/java/picard/illumina/CheckIlluminaDirectory.java @@ -77,7 +77,7 @@ "UNLESS the " + "individual records of the files themselves are spurious.", shortName = "DT", optional = true) - public final Set DATA_TYPES = new TreeSet(); + public final Set DATA_TYPES = new TreeSet<>(); @Option(doc = ReadStructure.PARAMETER_DOC + " Note: If you want to check whether or not a future IlluminaBasecallsToSam or " + "ExtractIlluminaBarcodes run will fail then be sure to use the exact same READ_STRUCTURE that you would pass to these programs " + @@ -94,14 +94,14 @@ @Option(doc = "A flag to determine whether or not to create fake versions of the missing files.", shortName = "F", optional = true) - public Boolean FAKE_FILES = false; + public final Boolean FAKE_FILES = false; @Option(doc = "A flag to create symlinks to the loc file for the X Ten for each tile.", shortName = "X", optional = true) - public Boolean LINK_LOCS = false; + public final Boolean LINK_LOCS = false; @Option(doc = "Use the new converter. Defaults to false", optional = true) - public boolean USE_NEW_CONVERTER = false; + public final boolean USE_NEW_CONVERTER = false; /** * Required main method implementation. @@ -117,7 +117,7 @@ protected int doWork() { DATA_TYPES.addAll(Arrays.asList(IlluminaBasecallsConverter.DATA_TYPES_NO_BARCODE)); } - final List failingLanes = new ArrayList(); + final List failingLanes = new ArrayList<>(); int totalFailures = 0; final int[] expectedCycles = new OutputMapping(readStructure).getOutputCycles(); @@ -127,14 +127,14 @@ protected int doWork() { for (final Integer lane : LANES) { if (USE_NEW_CONVERTER) { - List tiles = new ArrayList<>(); + final List tiles = new ArrayList<>(); - File laneDir = new File(BASECALLS_DIR, IlluminaFileUtil.longLaneStr(lane)); + final File laneDir = new File(BASECALLS_DIR, IlluminaFileUtil.longLaneStr(lane)); - File[] cycleDirs = IOUtil.getFilesMatchingRegexp(laneDir, IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN); + final File[] cycleDirs = IOUtil.getFilesMatchingRegexp(laneDir, IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN); //check all bcls/cbcls - List cbcls = new ArrayList<>(); + final List cbcls = new ArrayList<>(); Arrays.asList(cycleDirs) .forEach(cycleDir -> cbcls.addAll( Arrays.asList(IOUtil.getFilesMatchingRegexp( @@ -142,11 +142,11 @@ protected int doWork() { IOUtil.assertFilesAreReadable(cbcls); //check all pf filter files - Pattern laneTileRegex = Pattern.compile(ParameterizedFileUtil.escapePeriods( + final 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()); + final File[] filterFiles = getTiledFiles(laneDir, laneTileRegex); + for (final File filterFile : filterFiles) { + final Matcher tileMatcher = laneTileRegex.matcher(filterFile.getName()); if (tileMatcher.matches()) { tiles.add(Integer.valueOf(tileMatcher.group(1))); } @@ -155,24 +155,24 @@ protected int doWork() { 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<>(); + final File locsFile = new File(BASECALLS_DIR.getParentFile(), "s.locs"); + final LocsFileReader locsFileReader = new LocsFileReader(locsFile); + final List locs = new ArrayList<>(); while (locsFileReader.hasNext()) { locs.add(locsFileReader.next()); } - Map filterFileMap = new HashMap<>(); - for (File filterFile : filterFiles) { + final Map filterFileMap = new HashMap<>(); + for (final File filterFile : filterFiles) { filterFileMap.put(fileToTile(filterFile.getName()), filterFile); } - OutputMapping outputMapping = new OutputMapping(readStructure); + final OutputMapping outputMapping = new OutputMapping(readStructure); - CbclReader reader = new CbclReader(cbcls, filterFileMap, readStructure.readLengths, tiles.get(0), locs, outputMapping.getOutputCycles(), true); + final CbclReader reader = new CbclReader(cbcls, filterFileMap, readStructure.readLengths, tiles.get(0), locs, outputMapping.getOutputCycles(), true); reader.getAllTiles().forEach((key, value) -> { - List fileForCycle = reader.getFilesForCycle(key); + final 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(); @@ -293,7 +293,7 @@ private static final int verifyLane(final IlluminaFileUtil fileUtil, final List< } } log.info("Could not find a format with available files for the following data types: " + StringUtil - .join(", ", new ArrayList(unmatchedDataTypes))); + .join(", ", new ArrayList<>(unmatchedDataTypes))); numFailures += unmatchedDataTypes.size(); } @@ -318,7 +318,7 @@ private static final int verifyLane(final IlluminaFileUtil fileUtil, final List< @Override protected String[] customCommandLineValidation() { IOUtil.assertDirectoryIsReadable(BASECALLS_DIR); - final List errors = new ArrayList(); + final List errors = new ArrayList<>(); for (final Integer lane : LANES) { if (lane < 1) { diff --git a/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java b/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java index f8930eaa5..b414f4307 100644 --- a/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java +++ b/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java @@ -57,21 +57,22 @@ import java.util.TreeMap; import java.util.regex.Matcher; import java.util.regex.Pattern; - -import static picard.illumina.NewIlluminaBasecallsConverter.getTiledFiles; - -/*** - - * A Command line tool to collect Illumina Basecalling metrics for a sequencing run - - * Requires a Lane and an input file of Barcodes to expect. - - * Outputs metrics: - - * * Mean Clusters Per Tile - - * * Standard Deviation of Clusters Per Tile - - * * Mean Pf Clusters Per Tile - - * * Standard Deviation of Pf Clusters Per Tile - - * * Mean Percentage of Pf Clusters Per Tile - - * * Standard Deviation of Percentage of Pf Clusters Per Tile - - */ - +import java.util.stream.Collectors; + + +/** + * A Command line tool to collect Illumina Basecalling metrics for a sequencing run + * Requires a Lane and an input file of Barcodes to expect. + * Outputs metrics: + *
    + *
  • Mean Clusters Per Tile
    • + *
  • Standard Deviation of Clusters Per Tile
    • + *
  • Mean Pf Clusters Per Tile
    • + *
  • Standard Deviation of Pf Clusters Per Tile
    • + *
  • Mean Percentage of Pf Clusters Per Tile
    • + *
  • Standard Deviation of Percentage of Pf Clusters Per Tile
    • + *
+ */ @CommandLineProgramProperties( usage = CollectIlluminaBasecallingMetrics.USAGE_SUMMARY + CollectIlluminaBasecallingMetrics.USAGE_DETAILS, usageShort = CollectIlluminaBasecallingMetrics.USAGE_SUMMARY, @@ -127,8 +128,8 @@ @Option(doc = "The file to which the collected metrics are written", shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, optional = true) public File OUTPUT; - @Option(doc = "Use the new converter", optional = true) - public boolean USE_NEW_CONVERTER = false; + @Option(doc = "Use the (experimental) new converter that current supports CBCLs output from the NovaSeq", optional = true) + public final boolean USE_NEW_CONVERTER = false; private int barcodeLength = 0; private String unmatched_barcode; @@ -138,7 +139,7 @@ private static final String BARCODE_SEQUENCE_COLUMN_NAME_STUB = "barcode_sequence_"; public CollectIlluminaBasecallingMetrics() { - this.barcodeToMetricCounts = new TreeMap(); + this.barcodeToMetricCounts = new TreeMap<>(); } @Override @@ -203,74 +204,78 @@ protected int doWork() { //Initialize data provider, iterate over clusters, and collect statistics // BaseIlluminaDataProvider provider; if (USE_NEW_CONVERTER) { - File laneDir = new File(BASECALLS_DIR, IlluminaFileUtil.longLaneStr(LANE)); + setupNewDataProvider(factory); + } else { + final BaseIlluminaDataProvider provider = factory.makeDataProvider(); - File[] cycleDirs = IOUtil.getFilesMatchingRegexp(laneDir, IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN); + while (provider.hasNext()) { + final ClusterData cluster = provider.next(); + addCluster(cluster); + } + } - //CBCLs - List cbcls = new ArrayList<>(); - Arrays.asList(cycleDirs) - .forEach(cycleDir -> cbcls.addAll( - Arrays.asList(IOUtil.getFilesMatchingRegexp( - cycleDir, "^" + IlluminaFileUtil.longLaneStr(LANE) + "_(\\d{1,5}).cbcl$")))); + onComplete(); + return 0; + } - if (cbcls.size() == 0) { - throw new PicardException("No CBCL files found."); - } + private void setupNewDataProvider(final IlluminaDataProviderFactory factory) { + final File laneDir = new File(BASECALLS_DIR, IlluminaFileUtil.longLaneStr(LANE)); - IOUtil.assertFilesAreReadable(cbcls); + final File[] cycleDirs = IOUtil.getFilesMatchingRegexp(laneDir, IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN); - //locs - List locs = new ArrayList<>(); - File locsFile = new File(BASECALLS_DIR.getParentFile(), "s.locs"); - try (LocsFileReader locsFileReader = new LocsFileReader(locsFile)) { - while (locsFileReader.hasNext()) { - locs.add(locsFileReader.next()); - } - } - IOUtil.assertFileIsReadable(locsFile); - - //filter - Pattern laneTileRegex = Pattern.compile(ParameterizedFileUtil.escapePeriods( - ParameterizedFileUtil.makeLaneTileRegex(".filter", LANE))); - File[] filterFiles = getTiledFiles(laneDir, laneTileRegex); - - IOUtil.assertFilesAreReadable(Arrays.asList(filterFiles)); - Pattern barcodeRegex = Pattern.compile(ParameterizedFileUtil.escapePeriods( - ParameterizedFileUtil.makeLaneTileRegex("_barcode.txt", LANE))); - Map barcodesFiles = new HashMap<>(); - for (File barcodeFile : getTiledFiles(laneDir, barcodeRegex)) { - Matcher tileMatcher = barcodeRegex.matcher(barcodeFile.getName()); - if (tileMatcher.matches()) { - barcodesFiles.put(Integer.valueOf(tileMatcher.group(1)), barcodeFile); - } - } + //CBCLs + final List cbcls = Arrays.stream(cycleDirs) + .flatMap(cycleDir -> Arrays.stream(IOUtil.getFilesMatchingRegexp(cycleDir, + "^" + IlluminaFileUtil.longLaneStr(LANE) + "_(\\d{1,5}).cbcl$"))).collect(Collectors.toList()); - factory.getAvailableTiles().forEach(tile -> { - File barcodeFile = barcodesFiles.get(tile); - BaseIlluminaDataProvider provider = factory.makeDataProvider(cbcls, locs, filterFiles, tile, barcodeFile); - while (provider.hasNext()) { - addCluster(provider.next()); - } - }); - } else { - BaseIlluminaDataProvider provider = factory.makeDataProvider(); + if (cbcls.size() == 0) { + throw new PicardException("No CBCL files found."); + } - while (provider.hasNext()) { - final ClusterData cluster = provider.next(); - addCluster(cluster); + IOUtil.assertFilesAreReadable(cbcls); + + //locs + final List locs = new ArrayList<>(); + final File locsFile = new File(BASECALLS_DIR.getParentFile(), AbstractIlluminaPositionFileReader.S_LOCS_FILE); + IOUtil.assertFileIsReadable(locsFile); + try (LocsFileReader locsFileReader = new LocsFileReader(locsFile)) { + while (locsFileReader.hasNext()) { + locs.add(locsFileReader.next()); } } + //filter + final Pattern laneTileRegex = Pattern.compile(ParameterizedFileUtil.escapePeriods( + ParameterizedFileUtil.makeLaneTileRegex(".filter", LANE))); + final File[] filterFiles = NewIlluminaBasecallsConverter.getTiledFiles(laneDir, laneTileRegex); - onComplete(); - return 0; + IOUtil.assertFilesAreReadable(Arrays.asList(filterFiles)); + final Pattern barcodeRegex = Pattern.compile(ParameterizedFileUtil.escapePeriods( + ParameterizedFileUtil.makeLaneTileRegex("_barcode.txt", LANE))); + + + final Map barcodesFiles = new HashMap<>(); + IOUtil.assertFilesAreReadable(new ArrayList<>(barcodesFiles.values())); + for (final File barcodeFile : NewIlluminaBasecallsConverter.getTiledFiles(laneDir, barcodeRegex)) { + final Matcher tileMatcher = barcodeRegex.matcher(barcodeFile.getName()); + if (tileMatcher.matches()) { + barcodesFiles.put(Integer.valueOf(tileMatcher.group(1)), barcodeFile); + } + } + + factory.getAvailableTiles().forEach(tile -> { + final File barcodeFile = barcodesFiles.get(tile); + final BaseIlluminaDataProvider provider = factory.makeDataProvider(cbcls, locs, filterFiles, tile, barcodeFile); + while (provider.hasNext()) { + addCluster(provider.next()); + } + }); } /*** * Process new cluster of Illumina data - increment a running counter of data */ - private synchronized void addCluster(final ClusterData cluster) { + private void addCluster(final ClusterData cluster) { //compute hash of Barcode and Lane for key String barcode = cluster.getMatchedBarcode(); if (barcode == null) barcode = unmatched_barcode; @@ -297,8 +302,9 @@ private void onComplete() { counts.addMetricsToFile(file); allLaneCounts.addIlluminaMetricCounts(counts); } - if (!barcodeToMetricCounts.keySet().contains("")) + if (!barcodeToMetricCounts.keySet().contains("")) { allLaneCounts.addMetricsToFile(file); // detect non-indexed case + } file.write(OUTPUT); } catch (final Exception ex) { throw new PicardException("Error writing output file " + OUTPUT.getPath(), ex); @@ -321,8 +327,8 @@ public static void main(final String[] argv) { final IlluminaBasecallingMetrics metrics; public IlluminaMetricCounts(final String barcode, final String barcodeName, final Integer laneNumber) { - this.tileToClusterHistogram = new Histogram(); - this.tileToPfClusterHistogram = new Histogram(); + this.tileToClusterHistogram = new Histogram<>(); + this.tileToPfClusterHistogram = new Histogram<>(); this.metrics = new IlluminaBasecallingMetrics(); this.metrics.MOLECULAR_BARCODE_SEQUENCE_1 = barcode; this.metrics.MOLECULAR_BARCODE_NAME = barcodeName; @@ -366,8 +372,9 @@ private void onComplete() { final ReadStructure readStructure = new ReadStructure(READ_STRUCTURE); int templateBaseCountPerCluster = 0; - for (int i = 0; i < readStructure.templates.length(); i++) + for (int i = 0; i < readStructure.templates.length(); i++) { templateBaseCountPerCluster += readStructure.templates.get(i).length; + } metrics.TOTAL_READS = metrics.TOTAL_CLUSTERS * readStructure.templates.length(); metrics.PF_READS = metrics.PF_CLUSTERS * readStructure.templates.length(); metrics.TOTAL_BASES = metrics.TOTAL_CLUSTERS * templateBaseCountPerCluster; diff --git a/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java b/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java index f66ae1dd8..f3a7f8d6b 100644 --- a/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java +++ b/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java @@ -65,6 +65,7 @@ import java.util.concurrent.ThreadPoolExecutor; import java.util.concurrent.TimeUnit; import java.util.regex.Pattern; +import java.util.stream.Collectors; import static picard.illumina.NewIlluminaBasecallsConverter.getTiledFiles; @@ -149,7 +150,7 @@ @Option(doc = "Barcode sequence. These must be unique, and all the same length. This cannot be used with reads that " + "have more than one barcode; use BARCODE_FILE in that case. ", mutex = {"BARCODE_FILE"}) - public List BARCODE = new ArrayList(); + public final List BARCODE = new ArrayList<>(); @Option(doc = "Tab-delimited file of barcode sequences, barcode name and, optionally, library name. " + "Barcodes must be unique and all the same length. Column headers must be 'barcode_sequence_1', " + @@ -160,31 +161,31 @@ public File METRICS_FILE; @Option(doc = "Maximum mismatches for a barcode to be considered a match.") - public int MAX_MISMATCHES = 1; + public final 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; + public final 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; + public final int MAX_NO_CALLS = 2; @Option(shortName = "Q", doc = "Minimum base quality. Any barcode bases falling below this quality will be considered a mismatch even in the bases match.") - public int MINIMUM_BASE_QUALITY = 0; + public final int MINIMUM_BASE_QUALITY = 0; @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; + public final int MINIMUM_QUALITY = BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY; @Option(shortName = "GZIP", doc = "Compress output s_l_t_barcode.txt files using gzip and append a .gz extension to the file names.") - public boolean COMPRESS_OUTPUTS = false; + public final boolean COMPRESS_OUTPUTS = false; @Option(doc = "Run this many PerTileBarcodeExtractors in parallel. If NUM_PROCESSORS = 0, number of cores is automatically set to " + "the number of cores available on the machine. If NUM_PROCESSORS < 0 then the number of cores used will be " + "the number available on the machine less NUM_PROCESSORS.") - public int NUM_PROCESSORS = 1; + public final int NUM_PROCESSORS = 1; - @Option(doc = "Use the new converter", optional = true) - public boolean USE_NEW_CONVERTER = false; + @Option(doc = "Use the (experimental) new converter that current supports CBCLs output from the NovaSeq", optional = true) + public final boolean USE_NEW_CONVERTER = false; private static final Log LOG = Log.getInstance(ExtractIlluminaBarcodes.class); @@ -195,7 +196,7 @@ private IlluminaDataProviderFactory factory; - private final Map barcodeToMetrics = new LinkedHashMap(); + private final Map barcodeToMetrics = new LinkedHashMap<>(); private final NumberFormat tileNumberFormatter = NumberFormat.getNumberInstance(); private BclQualityEvaluationStrategy bclQualityEvaluationStrategy; @@ -240,16 +241,14 @@ protected int doWork() { final List extractors = new ArrayList<>(factory.getAvailableTiles().size()); if (USE_NEW_CONVERTER) { - File laneDir = new File(BASECALLS_DIR, IlluminaFileUtil.longLaneStr(LANE)); + final File laneDir = new File(BASECALLS_DIR, IlluminaFileUtil.longLaneStr(LANE)); - File[] cycleDirs = IOUtil.getFilesMatchingRegexp(laneDir, IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN); + final File[] cycleDirs = IOUtil.getFilesMatchingRegexp(laneDir, IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN); //CBCLs - List cbcls = new ArrayList<>(); - Arrays.asList(cycleDirs) - .forEach(cycleDir -> cbcls.addAll( - Arrays.asList(IOUtil.getFilesMatchingRegexp( - cycleDir, "^" + IlluminaFileUtil.longLaneStr(LANE) + "_(\\d{1,5}).cbcl$")))); + final List cbcls = Arrays.stream(cycleDirs) + .flatMap(cycleDir -> Arrays.stream(IOUtil.getFilesMatchingRegexp(cycleDir, + "^" + IlluminaFileUtil.longLaneStr(LANE) + "_(\\d{1,5}).cbcl$"))).collect(Collectors.toList()); if (cbcls.size() == 0) { throw new PicardException("No CBCL files found."); @@ -258,19 +257,19 @@ protected int doWork() { IOUtil.assertFilesAreReadable(cbcls); //locs - List locs = new ArrayList<>(); - File locsFile = new File(BASECALLS_DIR.getParentFile(), "s.locs"); + final List locs = new ArrayList<>(); + final File locsFile = new File(BASECALLS_DIR.getParentFile(), AbstractIlluminaPositionFileReader.S_LOCS_FILE); + IOUtil.assertFileIsReadable(locsFile); try (LocsFileReader locsFileReader = new LocsFileReader(locsFile)) { while (locsFileReader.hasNext()) { locs.add(locsFileReader.next()); } } - IOUtil.assertFileIsReadable(locsFile); //filter - Pattern laneTileRegex = Pattern.compile(ParameterizedFileUtil.escapePeriods( + final Pattern laneTileRegex = Pattern.compile(ParameterizedFileUtil.escapePeriods( ParameterizedFileUtil.makeLaneTileRegex(".filter", LANE))); - File[] filterFiles = getTiledFiles(laneDir, laneTileRegex); + final File[] filterFiles = getTiledFiles(laneDir, laneTileRegex); IOUtil.assertFilesAreReadable(Arrays.asList(filterFiles)); @@ -344,7 +343,7 @@ protected int doWork() { finalizeMetrics(barcodeToMetrics, noMatchMetric); // Warn about minimum qualities and assert that we've achieved the minimum. - for (Map.Entry entry : bclQualityEvaluationStrategy.getPoorQualityFrequencies().entrySet()) { + for (final Map.Entry entry : bclQualityEvaluationStrategy.getPoorQualityFrequencies().entrySet()) { LOG.warn(String.format("Observed low quality of %s %s times.", entry.getKey(), entry.getValue())); } bclQualityEvaluationStrategy.assertMinimumQualities(); @@ -433,7 +432,7 @@ private File getBarcodeFile(final int tile) { */ @Override protected String[] customCommandLineValidation() { - final ArrayList messages = new ArrayList(); + final ArrayList messages = new ArrayList<>(); this.bclQualityEvaluationStrategy = new BclQualityEvaluationStrategy(MINIMUM_QUALITY); @@ -455,7 +454,7 @@ private File getBarcodeFile(final int tile) { if (BARCODE_FILE != null) { parseBarcodeFile(messages); } else { - final Set barcodes = new HashSet(); + final Set barcodes = new HashSet<>(); for (final String barcode : BARCODE) { if (barcodes.contains(barcode)) { messages.add("Barcode " + barcode + " specified more than once."); @@ -496,7 +495,7 @@ private void parseBarcodeFile(final ArrayList messages) { final boolean hasBarcodeName = barcodesParser.hasColumn(BARCODE_NAME_COLUMN); final boolean hasLibraryName = barcodesParser.hasColumn(LIBRARY_NAME_COLUMN); final int numBarcodes = readStructure.sampleBarcodes.length(); - final Set barcodes = new HashSet(); + final Set barcodes = new HashSet<>(); for (final TabbedTextFileWithHeaderParser.Row row : barcodesParser) { final String[] bcStrings = new String[numBarcodes]; int barcodeNum = 1; @@ -676,9 +675,9 @@ public PerTileBarcodeExtractor( final int maxNoCalls, final int maxMismatches, final int minMismatchDelta, - List cbcls, - List locs, - File[] filterFiles) { + final List cbcls, + final List locs, + final File[] filterFiles) { this.tile = tile; this.barcodeFile = barcodeFile; this.usingQualityScores = minimumBaseQuality > 0; @@ -742,7 +741,7 @@ public PerTileBarcodeExtractor( this.maxMismatches = maxMismatches; this.minMismatchDelta = minMismatchDelta; this.minimumBaseQuality = minimumBaseQuality; - this.metrics = new LinkedHashMap(barcodeToMetrics.size()); + this.metrics = new LinkedHashMap<>(barcodeToMetrics.size()); for (final String key : barcodeToMetrics.keySet()) { this.metrics.put(key, BarcodeMetric.copy(barcodeToMetrics.get(key))); } @@ -913,14 +912,11 @@ public static BarcodeMatch findBestBarcodeAndUpdateMetrics(final byte[][] readSu * * @return how many bases did not match */ - private static int countMismatches(final byte[][] barcodeBytes, final byte[][] readSubsequence, final byte[][] qualities, int minimumBaseQuality) { + private static int countMismatches(final byte[][] barcodeBytes, final byte[][] readSubsequence, final byte[][] qualities, final int minimumBaseQuality) { int numMismatches = 0; for (int j = 0; j < barcodeBytes.length; j++) { - for (int i = 0; i < barcodeBytes[j].length; ++i) { - if (readSubsequence[j].length <= i) { - break; - } + for (int i = 0; (i < barcodeBytes[j].length && readSubsequence[j].length <= i); ++i) { if (SequenceUtil.isNoCall(readSubsequence[j][i])) { continue; } diff --git a/src/main/java/picard/illumina/IlluminaBasecallsToSam.java b/src/main/java/picard/illumina/IlluminaBasecallsToSam.java index 2da8c2421..7b27fdb78 100644 --- a/src/main/java/picard/illumina/IlluminaBasecallsToSam.java +++ b/src/main/java/picard/illumina/IlluminaBasecallsToSam.java @@ -304,12 +304,12 @@ private void initialize() { FIRST_TILE, TILE_LIMIT, new QueryNameComparator(), new Codec(numOutputRecords), SAMRecordsForCluster.class, bclQualityEvaluationStrategy, - this.APPLY_EAMSS_FILTER, INCLUDE_NON_PF_READS, IGNORE_UNEXPECTED_BARCODES); + APPLY_EAMSS_FILTER, INCLUDE_NON_PF_READS, IGNORE_UNEXPECTED_BARCODES); } 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); + bclQualityEvaluationStrategy, 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 diff --git a/src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java b/src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java index 673a09daa..2c3b968e8 100644 --- a/src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java +++ b/src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java @@ -58,7 +58,7 @@ * @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, */ - public NewIlluminaBasecallsConverter(final File basecallsDir, File barcodesDir, final int lane, + public NewIlluminaBasecallsConverter(final File basecallsDir, final File barcodesDir, final int lane, final ReadStructure readStructure, final Map> barcodeRecordWriterMap, final boolean demultiplex, @@ -79,13 +79,11 @@ public NewIlluminaBasecallsConverter(final File basecallsDir, File barcodesDir, barcodesDir, lane, readStructure, bclQualityEvaluationStrategy)); this.tiles = new ArrayList<>(); - barcodeRecordWriterMap.keySet().forEach(barcode -> { - barcodeWriterThreads.put(barcode, new ThreadPoolExecutorWithExceptions(1)); - }); + barcodeRecordWriterMap.keySet().forEach(barcode -> barcodeWriterThreads.put(barcode, new ThreadPoolExecutorWithExceptions(1))); - File laneDir = new File(basecallsDir, IlluminaFileUtil.longLaneStr(lane)); + final File laneDir = new File(basecallsDir, IlluminaFileUtil.longLaneStr(lane)); - File[] cycleDirs = IOUtil.getFilesMatchingRegexp(laneDir, IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN); + final File[] cycleDirs = IOUtil.getFilesMatchingRegexp(laneDir, IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN); //CBCLs cbcls = new ArrayList<>(); @@ -101,7 +99,7 @@ public NewIlluminaBasecallsConverter(final File basecallsDir, File barcodesDir, IOUtil.assertFilesAreReadable(cbcls); //locs - File locsFile = new File(basecallsDir.getParentFile(), "s.locs"); + final File locsFile = new File(basecallsDir.getParentFile(), "s.locs"); try (LocsFileReader locsFileReader = new LocsFileReader(locsFile)) { while (locsFileReader.hasNext()) { locs.add(locsFileReader.next()); @@ -110,11 +108,11 @@ public NewIlluminaBasecallsConverter(final File basecallsDir, File barcodesDir, IOUtil.assertFileIsReadable(locsFile); //filter - Pattern filterRegex = Pattern.compile(ParameterizedFileUtil.escapePeriods( + final Pattern filterRegex = Pattern.compile(ParameterizedFileUtil.escapePeriods( ParameterizedFileUtil.makeLaneTileRegex(".filter", lane))); filterFiles = getTiledFiles(laneDir, filterRegex); - for (File filterFile : filterFiles) { - Matcher tileMatcher = filterRegex.matcher(filterFile.getName()); + for (final File filterFile : filterFiles) { + final Matcher tileMatcher = filterRegex.matcher(filterFile.getName()); if (tileMatcher.matches()) { tiles.add(Integer.valueOf(tileMatcher.group(1))); } @@ -123,14 +121,16 @@ public NewIlluminaBasecallsConverter(final File basecallsDir, File barcodesDir, tiles.sort(TILE_NUMBER_COMPARATOR); if (demultiplex) { - Pattern barcodeRegex = Pattern.compile(ParameterizedFileUtil.escapePeriods( + final Pattern barcodeRegex = Pattern.compile(ParameterizedFileUtil.escapePeriods( ParameterizedFileUtil.makeLaneTileRegex("_barcode.txt(\\.gz|\\.bz2)?", lane))); - File[] barcodeTileFiles = getTiledFiles(barcodesDir, barcodeRegex); + final File[] barcodeTileFiles = getTiledFiles(barcodesDir, barcodeRegex); if (barcodeTileFiles.length != tiles.size()) { - throw new PicardException("Barcode files are required for each tile."); + throw new PicardException(String.format( + "Barcode files are required for each tile. Found %d expected %d.", + barcodeTileFiles.length, tiles.size())); } - for (File barcodeFile : barcodeTileFiles) { - Matcher tileMatcher = barcodeRegex.matcher(barcodeFile.getName()); + for (final File barcodeFile : barcodeTileFiles) { + final Matcher tileMatcher = barcodeRegex.matcher(barcodeFile.getName()); if (tileMatcher.matches()) { barcodesFiles.put(Integer.valueOf(tileMatcher.group(1)), barcodeFile); } @@ -141,23 +141,23 @@ public NewIlluminaBasecallsConverter(final File basecallsDir, File barcodesDir, setTileLimits(firstTile, tileLimit); } - public static File[] getTiledFiles(File baseDirectory, Pattern pattern) { + public static File[] getTiledFiles(final File baseDirectory, final Pattern pattern) { return IOUtil.getFilesMatchingRegexp(baseDirectory, pattern); } @Override public void doTileProcessing() { - ThreadPoolExecutor completedWorkExecutor = new ThreadPoolExecutorWithExceptions(1); + final ThreadPoolExecutor completedWorkExecutor = new ThreadPoolExecutorWithExceptions(1); - CompletedWorkChecker workChecker = new CompletedWorkChecker(); + final CompletedWorkChecker workChecker = new CompletedWorkChecker(); completedWorkExecutor.submit(workChecker); completedWorkExecutor.shutdown(); //thread by surface tile - ThreadPoolExecutor tileProcessingExecutor = new ThreadPoolExecutorWithExceptions(numThreads); + final ThreadPoolExecutor tileProcessingExecutor = new ThreadPoolExecutorWithExceptions(numThreads); - for (Integer tile : tiles) { + for (final Integer tile : tiles) { tileProcessingExecutor.submit(new TileProcessor(tile, barcodesFiles.get(tile))); } @@ -170,14 +170,14 @@ public void doTileProcessing() { barcodeWriterThreads.forEach((barcode, executor) -> awaitThreadPoolTermination(barcode + " writer", executor)); } - private void awaitThreadPoolTermination(String executorName, ThreadPoolExecutor executorService) { + private void awaitThreadPoolTermination(final String executorName, final 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) { + } catch (final InterruptedException e) { e.printStackTrace(); } } @@ -187,8 +187,8 @@ private void awaitThreadPoolTermination(String executorName, ThreadPoolExecutor private final ConvertedClusterDataWriter writer; private final String barcode; - RecordWriter(ConvertedClusterDataWriter writer, - SortingCollection recordCollection, String barcode) { + RecordWriter(final ConvertedClusterDataWriter writer, + final SortingCollection recordCollection, final String barcode) { this.writer = writer; this.recordCollection = recordCollection; this.barcode = barcode; @@ -196,7 +196,7 @@ private void awaitThreadPoolTermination(String executorName, ThreadPoolExecutor @Override public void run() { - for (CLUSTER_OUTPUT_RECORD record : recordCollection) { + for (final CLUSTER_OUTPUT_RECORD record : recordCollection) { writer.write(record); writeProgressLogger.record(null, 0); } @@ -211,7 +211,7 @@ public String getBarcode() { private final ConvertedClusterDataWriter writer; private final String barcode; - private Closer(ConvertedClusterDataWriter writer, String barcode) { + private Closer(final ConvertedClusterDataWriter writer, final String barcode) { this.writer = writer; this.barcode = barcode; } @@ -228,7 +228,7 @@ public void run() { private final Map> barcodeToRecordCollection = new HashMap<>(); private final File barcodeFile; - TileProcessor(int tileNum, File barcodeFile) { + TileProcessor(final int tileNum, final File barcodeFile) { this.tileNum = tileNum; this.barcodeFile = barcodeFile; } @@ -246,10 +246,10 @@ public void run() { dataProvider.close(); - List writerList = new ArrayList<>(); + final List writerList = new ArrayList<>(); barcodeToRecordCollection.forEach((barcode, value) -> { value.doneAdding(); - ConvertedClusterDataWriter writer = barcodeRecordWriterMap.get(barcode); + final ConvertedClusterDataWriter writer = barcodeRecordWriterMap.get(barcode); writerList.add(new RecordWriter(writer, value, barcode)); }); @@ -298,7 +298,7 @@ private synchronized void addRecord(final String barcode, final CLUSTER_OUTPUT_R @Override public void run() { while (currentTileIndex < tiles.size()) { - Integer currentTile = tiles.get(currentTileIndex); + final 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)); @@ -306,7 +306,7 @@ public void run() { } else { try { Thread.sleep(5000); - } catch (InterruptedException e) { + } catch (final InterruptedException e) { throw new PicardException(e.getMessage(), e); } } diff --git a/src/main/java/picard/illumina/parser/readers/CbclReader.java b/src/main/java/picard/illumina/parser/readers/CbclReader.java index 490b1e2fb..a8f87e7c7 100644 --- a/src/main/java/picard/illumina/parser/readers/CbclReader.java +++ b/src/main/java/picard/illumina/parser/readers/CbclReader.java @@ -75,7 +75,7 @@ private final Map> cachedFilter = new HashMap<>(); private final Map> surfaceToTileToCbclMap; private int headerSize; - private Map> allTiles = new HashMap<>(); + private final Map> allTiles = new HashMap<>(); private final int[] outputCycles; private static final int INITIAL_HEADER_SIZE = 6; @@ -83,7 +83,7 @@ private static final Pattern PATTERN = Pattern.compile("^.+C(\\d{1,4}).+L(\\d{1,3})_(\\d).cbcl$"); public CbclReader(final List cbcls, final Map filterFileMap, final int[] outputLengths, - int tileNum, List locs, int[] outputCycles, boolean headerOnly) { + final int tileNum, final List locs, final int[] outputCycles, final boolean headerOnly) { super(outputLengths); this.outputCycles = outputCycles; @@ -102,12 +102,12 @@ public CbclReader(final List cbcls, final Map filterFileMap } } - private void readSurfaceTile(int tileNum, List locs, - boolean headerOnly) { + private void readSurfaceTile(final int tileNum, final List locs, + final boolean headerOnly) { log.info("Processing tile " + tileNum); try { - for (Map.Entry> entry : surfaceToTileToCbclMap.entrySet()) { - Map cycleMap = entry.getValue(); + for (final Map.Entry> entry : surfaceToTileToCbclMap.entrySet()) { + final Map cycleMap = entry.getValue(); for (int i = 0; i < cycles; i++) { //cycleMap is 1 indexed final ByteBuffer byteBuffer = ByteBuffer.allocate(INITIAL_HEADER_SIZE); @@ -126,7 +126,7 @@ private void readSurfaceTile(int tileNum, List> sortCbcls(List cbcls) { - Map> sortedMap = new TreeMap<>(); - for (File cbcl : cbcls) { - Matcher matcher = PATTERN.matcher(cbcl.getAbsolutePath()); + private Map> sortCbcls(final List cbcls) { + final Map> sortedMap = new TreeMap<>(); + for (final File cbcl : cbcls) { + final 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)); + final Integer surface = Integer.valueOf(matcher.group(3)); + final Integer cycle = Integer.valueOf(matcher.group(1)); if (sortedMap.containsKey(surface)) { sortedMap.get(surface).put(cycle, cbcl); } else { - Map cycleMap = new HashMap<>(); + final Map cycleMap = new HashMap<>(); cycleMap.put(cycle, cbcl); sortedMap.put(surface, cycleMap); } @@ -252,7 +252,7 @@ public CbclData next() { if (queue == null) { advance(); } - CbclData data = queue; + final CbclData data = queue; queue = null; return data; } @@ -266,11 +266,11 @@ public void close() { private void advance() { int totalCycleCount = 0; - CbclData data = new CbclData(outputLengths, cycleData[totalCycleCount].tileInfo.tileNum); + final 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++) { - CycleData currentCycleData = cycleData[totalCycleCount]; + final CycleData currentCycleData = cycleData[totalCycleCount]; if (cachedTilePosition[totalCycleCount] >= cachedTile[totalCycleCount].length || cachedTilePosition[totalCycleCount] >= cycleData[totalCycleCount].getTileInfo().getNumClustersInTile()) { @@ -278,7 +278,7 @@ private void advance() { return; } - int singleByte = cachedTile[totalCycleCount][cachedTilePosition[totalCycleCount]++]; + final int singleByte = cachedTile[totalCycleCount][cachedTilePosition[totalCycleCount]++]; decodeQualityBinnedBasecall(data, read, cycle, singleByte, currentCycleData); @@ -289,18 +289,18 @@ private void advance() { this.queue = data; } - private void cacheFilterAndLocs(TileData currentTileData, List locs) { - List filterValues = new ArrayList<>(); - FilterFileReader reader = new FilterFileReader(filterFileMap.get(currentTileData.tileNum)); - Iterator positionInfoIterator = locs.iterator(); + private void cacheFilterAndLocs(final TileData currentTileData, final List locs) { + final List filterValues = new ArrayList<>(); + final FilterFileReader reader = new FilterFileReader(filterFileMap.get(currentTileData.tileNum)); + final Iterator positionInfoIterator = locs.iterator(); while (reader.hasNext()) { filterValues.add(reader.next()); } - List positions = new ArrayList<>(); - for (boolean filterValue : filterValues) { - AbstractIlluminaPositionFileReader.PositionInfo info = positionInfoIterator.next(); + final List positions = new ArrayList<>(); + for (final boolean filterValue : filterValues) { + final AbstractIlluminaPositionFileReader.PositionInfo info = positionInfoIterator.next(); if (filterValue) { positions.add(info); } @@ -309,30 +309,30 @@ private void cacheFilterAndLocs(TileData currentTileData, List 0) { dataLeft -= stream.skip(dataLeft); } - int readBytes = stream.read(tileByteArray); + final int readBytes = stream.read(tileByteArray); if (readBytes != tileData.compressedBlockSize) { 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(Arrays.copyOfRange(tileByteArray, 0, readBytes)); + final ByteArrayInputStream byteInputStream = new ByteArrayInputStream(Arrays.copyOfRange(tileByteArray, 0, readBytes)); - GZIPInputStream gzipInputStream = new GZIPInputStream(byteInputStream, uncompressedByteArray.length); + final GZIPInputStream gzipInputStream = new GZIPInputStream(byteInputStream, uncompressedByteArray.length); int read; int totalRead = 0; try { @@ -340,7 +340,7 @@ private void cacheTile(int totalCycleCount, TileData tileData, CycleData current if (read == 0) break; totalRead += read; } - } catch (EOFException eofException) { + } catch (final 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 " @@ -353,7 +353,7 @@ private void cacheTile(int totalCycleCount, TileData tileData, CycleData current // Read uncompressed data from the buffer and expand each nibble into a full byte for ease of use int index = 0; - for (byte singleByte : uncompressedByteArray) { + for (final byte singleByte : uncompressedByteArray) { unNibbledByteArray[index] = (byte) (singleByte & 0x0f); index++; unNibbledByteArray[index] = (byte) ((singleByte >> 4) & 0x0f); @@ -364,16 +364,16 @@ private void cacheTile(int totalCycleCount, TileData tileData, CycleData current // Write buffer contents to cached tile array // if nonPF reads are included we need to strip them out if (!currentCycleData.pfExcluded) { - List filterDatas = cachedFilter.get(tileData.tileNum); + final List filterDatas = cachedFilter.get(tileData.tileNum); int sum = 0; - for (boolean b : filterDatas) { + for (final boolean b : filterDatas) { sum += b ? 1 : 0; } - byte[] filteredByteArray = new byte[sum]; + final byte[] filteredByteArray = new byte[sum]; int filterIndex = 0; int basecallIndex = 0; - for (boolean filterData : filterDatas) { - byte readByte = unNibbledByteArray[filterIndex]; + for (final boolean filterData : filterDatas) { + final byte readByte = unNibbledByteArray[filterIndex]; if (filterData) { filteredByteArray[basecallIndex] = readByte; basecallIndex++; @@ -395,8 +395,8 @@ public int getHeaderSize() { return headerSize; } - public List getFilesForCycle(int i) { - List cbclFiles = new ArrayList<>(); + public List getFilesForCycle(final int i) { + final List cbclFiles = new ArrayList<>(); surfaceToTileToCbclMap.values().forEach(map -> { if (map.containsKey(i)) { cbclFiles.add(map.get(i)); diff --git a/src/main/java/picard/util/ThreadPoolExecutorWithExceptions.java b/src/main/java/picard/util/ThreadPoolExecutorWithExceptions.java index 30f656b41..84513ba8c 100644 --- a/src/main/java/picard/util/ThreadPoolExecutorWithExceptions.java +++ b/src/main/java/picard/util/ThreadPoolExecutorWithExceptions.java @@ -9,24 +9,33 @@ import java.util.concurrent.ThreadPoolExecutor; import java.util.concurrent.TimeUnit; +/** + * This version of the thread pool executor will throw an exception if any of the internal jobs have throw exceptions + * while executing + */ public class ThreadPoolExecutorWithExceptions extends ThreadPoolExecutor { - public ThreadPoolExecutorWithExceptions(int threads) { + /** + * Creates a fixed size thread pool executor that will rethrow exceptions from submitted jobs. + * + * @param threads The number of threads in the executor pool. + */ + public ThreadPoolExecutorWithExceptions(final int threads) { super(threads, threads, 0, TimeUnit.SECONDS, new LinkedBlockingDeque<>()); } @Override - protected void afterExecute(Runnable r, Throwable t) { + protected void afterExecute(final Runnable r, Throwable t) { if (t == null && r instanceof Future) { try { - Future future = (Future) r; + final Future future = (Future) r; if (future.isDone()) { future.get(); } - } catch (CancellationException ce) { + } catch (final CancellationException ce) { t = ce; - } catch (ExecutionException ee) { + } catch (final ExecutionException ee) { t = ee.getCause(); - } catch (InterruptedException ie) { + } catch (final InterruptedException ie) { Thread.currentThread().interrupt(); // ignore/reset } } From 0597f85cf4c29187cbcde92a66dddccf5d94b3cb Mon Sep 17 00:00:00 2001 From: jacarey Date: Tue, 27 Jun 2017 16:16:28 -0400 Subject: [PATCH 3/6] Intellij got overzealous with finals. @Options can't be final --- .../java/picard/illumina/CheckIlluminaDirectory.java | 8 ++++---- .../illumina/CollectIlluminaBasecallingMetrics.java | 2 +- .../java/picard/illumina/ExtractIlluminaBarcodes.java | 18 +++++++++--------- 3 files changed, 14 insertions(+), 14 deletions(-) diff --git a/src/main/java/picard/illumina/CheckIlluminaDirectory.java b/src/main/java/picard/illumina/CheckIlluminaDirectory.java index afd6d07b0..43d1f3fc5 100644 --- a/src/main/java/picard/illumina/CheckIlluminaDirectory.java +++ b/src/main/java/picard/illumina/CheckIlluminaDirectory.java @@ -77,7 +77,7 @@ "UNLESS the " + "individual records of the files themselves are spurious.", shortName = "DT", optional = true) - public final Set DATA_TYPES = new TreeSet<>(); + public Set DATA_TYPES = new TreeSet<>(); @Option(doc = ReadStructure.PARAMETER_DOC + " Note: If you want to check whether or not a future IlluminaBasecallsToSam or " + "ExtractIlluminaBarcodes run will fail then be sure to use the exact same READ_STRUCTURE that you would pass to these programs " + @@ -94,14 +94,14 @@ @Option(doc = "A flag to determine whether or not to create fake versions of the missing files.", shortName = "F", optional = true) - public final Boolean FAKE_FILES = false; + public Boolean FAKE_FILES = false; @Option(doc = "A flag to create symlinks to the loc file for the X Ten for each tile.", shortName = "X", optional = true) - public final Boolean LINK_LOCS = false; + public Boolean LINK_LOCS = false; @Option(doc = "Use the new converter. Defaults to false", optional = true) - public final boolean USE_NEW_CONVERTER = false; + public boolean USE_NEW_CONVERTER = false; /** * Required main method implementation. diff --git a/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java b/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java index b414f4307..7ef8f489e 100644 --- a/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java +++ b/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java @@ -129,7 +129,7 @@ public File OUTPUT; @Option(doc = "Use the (experimental) new converter that current supports CBCLs output from the NovaSeq", optional = true) - public final boolean USE_NEW_CONVERTER = false; + public boolean USE_NEW_CONVERTER = false; private int barcodeLength = 0; private String unmatched_barcode; diff --git a/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java b/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java index f3a7f8d6b..5b74fbe89 100644 --- a/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java +++ b/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java @@ -150,7 +150,7 @@ @Option(doc = "Barcode sequence. These must be unique, and all the same length. This cannot be used with reads that " + "have more than one barcode; use BARCODE_FILE in that case. ", mutex = {"BARCODE_FILE"}) - public final List BARCODE = new ArrayList<>(); + public List BARCODE = new ArrayList<>(); @Option(doc = "Tab-delimited file of barcode sequences, barcode name and, optionally, library name. " + "Barcodes must be unique and all the same length. Column headers must be 'barcode_sequence_1', " + @@ -161,31 +161,31 @@ public File METRICS_FILE; @Option(doc = "Maximum mismatches for a barcode to be considered a match.") - public final int MAX_MISMATCHES = 1; + 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 final int MIN_MISMATCH_DELTA = 1; + public int MIN_MISMATCH_DELTA = 1; @Option(doc = "Maximum allowable number of no-calls in a barcode read before it is considered unmatchable.") - public final int MAX_NO_CALLS = 2; + public int MAX_NO_CALLS = 2; @Option(shortName = "Q", doc = "Minimum base quality. Any barcode bases falling below this quality will be considered a mismatch even in the bases match.") - public final int MINIMUM_BASE_QUALITY = 0; + public int MINIMUM_BASE_QUALITY = 0; @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 final int MINIMUM_QUALITY = BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY; + public int MINIMUM_QUALITY = BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY; @Option(shortName = "GZIP", doc = "Compress output s_l_t_barcode.txt files using gzip and append a .gz extension to the file names.") - public final boolean COMPRESS_OUTPUTS = false; + public boolean COMPRESS_OUTPUTS = false; @Option(doc = "Run this many PerTileBarcodeExtractors in parallel. If NUM_PROCESSORS = 0, number of cores is automatically set to " + "the number of cores available on the machine. If NUM_PROCESSORS < 0 then the number of cores used will be " + "the number available on the machine less NUM_PROCESSORS.") - public final int NUM_PROCESSORS = 1; + public int NUM_PROCESSORS = 1; @Option(doc = "Use the (experimental) new converter that current supports CBCLs output from the NovaSeq", optional = true) - public final boolean USE_NEW_CONVERTER = false; + public boolean USE_NEW_CONVERTER = false; private static final Log LOG = Log.getInstance(ExtractIlluminaBarcodes.class); From e7431d2f4964cf84b7bd9fba44a77c5d7f720f19 Mon Sep 17 00:00:00 2001 From: jacarey Date: Tue, 27 Jun 2017 16:31:37 -0400 Subject: [PATCH 4/6] Flip logic (oops) --- src/main/java/picard/illumina/ExtractIlluminaBarcodes.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java b/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java index 5b74fbe89..fb8e9cf6c 100644 --- a/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java +++ b/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java @@ -916,7 +916,7 @@ private static int countMismatches(final byte[][] barcodeBytes, final byte[][] r int numMismatches = 0; for (int j = 0; j < barcodeBytes.length; j++) { - for (int i = 0; (i < barcodeBytes[j].length && readSubsequence[j].length <= i); ++i) { + for (int i = 0; (i < barcodeBytes[j].length && readSubsequence[j].length > i); ++i) { if (SequenceUtil.isNoCall(readSubsequence[j][i])) { continue; } From fdff9d6997d1704b603635d4967874e79b844da1 Mon Sep 17 00:00:00 2001 From: jacarey Date: Wed, 28 Jun 2017 09:59:06 -0400 Subject: [PATCH 5/6] Fix up test dir. Remove USE_NEW_CONVERTER --- .../java/picard/illumina/BasecallsConverter.java | 6 +-- .../picard/illumina/CheckIlluminaDirectory.java | 5 +- .../CollectIlluminaBasecallingMetrics.java | 8 +-- .../illumina/CollectIlluminaLaneMetrics.java | 8 +-- .../picard/illumina/ExtractIlluminaBarcodes.java | 7 +-- .../illumina/IlluminaBasecallsConverter.java | 7 ++- .../picard/illumina/IlluminaBasecallsToFastq.java | 10 ++-- .../picard/illumina/IlluminaBasecallsToSam.java | 15 +++--- .../picard/illumina/IlluminaPhasingMetrics.java | 2 +- .../illumina/LanePhasingMetricsCollector.java | 2 +- .../illumina/NewIlluminaBasecallsConverter.java | 5 +- .../picard/illumina/parser/IlluminaFileUtil.java | 35 +++++++++---- .../picard/illumina/parser/readers/CbclReader.java | 3 ++ .../illumina/IlluminaBasecallsToFastqTest.java | 54 ++------------------- .../illumina/IlluminaBasecallsToSamTest.java | 49 ++----------------- .../illumina/parser/readers/CbclReaderTest.java | 35 ++++++++----- 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.../Intensities/BaseCalls/L001/C9.1/L001_2.cbcl | Bin .../Intensities/BaseCalls/L001/C90.1/L001_1.cbcl | Bin .../Intensities/BaseCalls/L001/C90.1/L001_2.cbcl | Bin .../Intensities/BaseCalls/L001/C91.1/L001_1.cbcl | Bin .../Intensities/BaseCalls/L001/C91.1/L001_2.cbcl | Bin .../Intensities/BaseCalls/L001/C92.1/L001_1.cbcl | Bin .../Intensities/BaseCalls/L001/C92.1/L001_2.cbcl | Bin .../Intensities/BaseCalls/L001/C93.1/L001_1.cbcl | Bin .../Intensities/BaseCalls/L001/C93.1/L001_2.cbcl | Bin .../Intensities/BaseCalls/L001/C94.1/L001_1.cbcl | Bin .../Intensities/BaseCalls/L001/C94.1/L001_2.cbcl | Bin .../Intensities/BaseCalls/L001/C95.1/L001_1.cbcl | Bin .../Intensities/BaseCalls/L001/C95.1/L001_2.cbcl | Bin .../Intensities/BaseCalls/L001/C96.1/L001_1.cbcl | Bin .../Intensities/BaseCalls/L001/C96.1/L001_2.cbcl | Bin .../Intensities/BaseCalls/L001/C97.1/L001_1.cbcl | Bin .../Intensities/BaseCalls/L001/C97.1/L001_2.cbcl | Bin .../Intensities/BaseCalls/L001/C98.1/L001_1.cbcl | Bin .../Intensities/BaseCalls/L001/C98.1/L001_2.cbcl | Bin .../Intensities/BaseCalls/L001/C99.1/L001_1.cbcl | Bin .../Intensities/BaseCalls/L001/C99.1/L001_2.cbcl | Bin .../Intensities/BaseCalls/L001/s_1_1101.filter | Bin .../Intensities/BaseCalls/L001/s_1_1102.filter | Bin .../Intensities/BaseCalls/s_1_1101_barcode.txt.gz | Bin .../Intensities/BaseCalls/s_1_1102_barcode.txt.gz | Bin .../Data/Intensities/s.locs | Bin .../fastq/CACCTAGTACTCGAGT.1.fastq | 0 .../fastq/CACCTAGTACTCGAGT.2.fastq | 0 .../fastq/CACCTAGTACTCGAGT.barcode_1.fastq | 0 .../fastq/CACCTAGTACTCGAGT.barcode_2.fastq | 0 .../fastq/CCCCGCTTTTGCGTGT.1.fastq | 0 .../fastq/CCCCGCTTTTGCGTGT.2.fastq | 0 .../fastq/CCCCGCTTTTGCGTGT.barcode_1.fastq | 0 .../fastq/CCCCGCTTTTGCGTGT.barcode_2.fastq | 0 .../fastq/GCTATAGTCCAGCAGC.1.fastq | 0 .../fastq/GCTATAGTCCAGCAGC.2.fastq | 0 .../fastq/GCTATAGTCCAGCAGC.barcode_1.fastq | 0 .../fastq/GCTATAGTCCAGCAGC.barcode_2.fastq | 0 .../fastq/NN.1.fastq | 0 .../fastq/NN.2.fastq | 0 .../fastq/NN.barcode_1.fastq | 0 .../fastq/NN.barcode_2.fastq | 0 .../fastq/TTGCGGCCGGTTTAAC.1.fastq | 0 .../fastq/TTGCGGCCGGTTTAAC.2.fastq | 0 .../fastq/TTGCGGCCGGTTTAAC.barcode_1.fastq | 0 .../fastq/TTGCGGCCGGTTTAAC.barcode_2.fastq | 0 .../fastq/barcode_double.params | 0 .../sams/CACCTAGTACTCGAGT.sam | 0 .../sams/CCCCGCTTTTGCGTGT.sam | 0 .../sams/GCTATAGTCCAGCAGC.sam | 0 .../sams/NN.sam | 0 .../sams/TTGCGGCCGGTTTAAC.sam | 0 .../sams/barcode_double.params | 0 684 files changed, 86 insertions(+), 165 deletions(-) rename testdata/picard/illumina/{125T8B8B125T_cbcl => 151T8B8B151T_cbcl}/Data/Intensities/BaseCalls/L001/C1.1/L001_1.cbcl (100%) rename testdata/picard/illumina/{125T8B8B125T_cbcl => 151T8B8B151T_cbcl}/Data/Intensities/BaseCalls/L001/C1.1/L001_2.cbcl (100%) rename testdata/picard/illumina/{125T8B8B125T_cbcl => 151T8B8B151T_cbcl}/Data/Intensities/BaseCalls/L001/C10.1/L001_1.cbcl (100%) rename testdata/picard/illumina/{125T8B8B125T_cbcl => 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151T8B8B151T_cbcl}/sams/barcode_double.params (100%) diff --git a/src/main/java/picard/illumina/BasecallsConverter.java b/src/main/java/picard/illumina/BasecallsConverter.java index b4abe6af6..305f7e1ee 100644 --- a/src/main/java/picard/illumina/BasecallsConverter.java +++ b/src/main/java/picard/illumina/BasecallsConverter.java @@ -20,7 +20,6 @@ final int maxReadsInRamPerTile; final boolean demultiplex; final List tmpDirs; - final boolean includeNonPfReads; final boolean ignoreUnexpectedBarcodes; final SortingCollection.Codec codecPrototype; final Class outputRecordClass; @@ -45,7 +44,6 @@ * @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, @@ -55,7 +53,6 @@ final boolean ignoreUnexpectedBarcodes, final boolean demultiplex, final Comparator outputRecordComparator, - final boolean includeNonPfReads, final BclQualityEvaluationStrategy bclQualityEvaluationStrategy, final Class outputRecordClass, final int numProcessors, @@ -68,7 +65,6 @@ this.ignoreUnexpectedBarcodes = ignoreUnexpectedBarcodes; this.demultiplex = demultiplex; this.outputRecordComparator = outputRecordComparator; - this.includeNonPfReads = includeNonPfReads; this.bclQualityEvaluationStrategy = bclQualityEvaluationStrategy; this.outputRecordClass = outputRecordClass; this.factory = factory; @@ -99,7 +95,7 @@ void setConverter(final ClusterDataConverter converter) { this.converter = converter; } - void setTileLimits(Integer firstTile, Integer tileLimit) { + void setTileLimits(final Integer firstTile, final Integer tileLimit) { if (firstTile != null) { int i; for (i = 0; i < tiles.size(); ++i) { diff --git a/src/main/java/picard/illumina/CheckIlluminaDirectory.java b/src/main/java/picard/illumina/CheckIlluminaDirectory.java index 43d1f3fc5..a01693cea 100644 --- a/src/main/java/picard/illumina/CheckIlluminaDirectory.java +++ b/src/main/java/picard/illumina/CheckIlluminaDirectory.java @@ -100,9 +100,6 @@ 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. */ @@ -126,7 +123,7 @@ protected int doWork() { log.info("Expected cycles: " + StringUtil.intValuesToString(expectedCycles)); for (final Integer lane : LANES) { - if (USE_NEW_CONVERTER) { + if (IlluminaFileUtil.hasCbcls(BASECALLS_DIR, lane)) { final List tiles = new ArrayList<>(); final File laneDir = new File(BASECALLS_DIR, IlluminaFileUtil.longLaneStr(lane)); diff --git a/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java b/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java index 7ef8f489e..092284e22 100644 --- a/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java +++ b/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java @@ -128,9 +128,6 @@ @Option(doc = "The file to which the collected metrics are written", shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, optional = true) public File OUTPUT; - @Option(doc = "Use the (experimental) new converter that current supports CBCLs output from the NovaSeq", optional = true) - public boolean USE_NEW_CONVERTER = false; - private int barcodeLength = 0; private String unmatched_barcode; private final SortedMap barcodeToMetricCounts; @@ -175,7 +172,7 @@ protected int doWork() { barcodeToMetricCounts.put(barcode.toString(), new IlluminaMetricCounts(barcode.toString(), barcodeName, LANE)); } } - if (USE_NEW_CONVERTER) { + if (IlluminaFileUtil.hasCbcls(BASECALLS_DIR, LANE)) { factory = new IlluminaDataProviderFactory(BASECALLS_DIR, BARCODES_DIR, LANE, readStructure, bclQualityEvaluationStrategy); } else { factory = barcodeToMetricCounts.isEmpty() @@ -202,8 +199,7 @@ protected int doWork() { unmatched_barcode = StringUtil.repeatCharNTimes('N', barcodeLength); //Initialize data provider, iterate over clusters, and collect statistics - // BaseIlluminaDataProvider provider; - if (USE_NEW_CONVERTER) { + if (IlluminaFileUtil.hasCbcls(BASECALLS_DIR, LANE)) { setupNewDataProvider(factory); } else { final BaseIlluminaDataProvider provider = factory.makeDataProvider(); diff --git a/src/main/java/picard/illumina/CollectIlluminaLaneMetrics.java b/src/main/java/picard/illumina/CollectIlluminaLaneMetrics.java index 4d4c60bbc..e8132a200 100644 --- a/src/main/java/picard/illumina/CollectIlluminaLaneMetrics.java +++ b/src/main/java/picard/illumina/CollectIlluminaLaneMetrics.java @@ -186,9 +186,9 @@ public static void collectLaneMetrics(final File runDirectory, final File output public static File writePhasingMetrics(final Map> laneTiles, final File outputDirectory, final String outputPrefix, final MetricsFile> phasingMetricsFile, - final String fileExtension, boolean isNovaSeq) { - laneTiles.entrySet().stream().forEach(entry -> IlluminaPhasingMetrics.getPhasingMetricsForTiles(entry.getKey().longValue(), - entry.getValue(), !isNovaSeq).forEach(phasingMetricsFile::addMetric)); + final String fileExtension, final boolean isNovaSeq) { + laneTiles.forEach((key, value) -> IlluminaPhasingMetrics.getPhasingMetricsForTiles(key.longValue(), + value, !isNovaSeq).forEach(phasingMetricsFile::addMetric)); return writeMetrics(phasingMetricsFile, outputDirectory, outputPrefix, IlluminaPhasingMetrics.getExtension() + fileExtension); } @@ -196,7 +196,7 @@ public static File writePhasingMetrics(final Map> laneTiles, final File outputDirectory, final String outputPrefix, final MetricsFile> laneMetricsFile, final String fileExtension) { - laneTiles.entrySet().stream().forEach(entry -> { + laneTiles.entrySet().forEach(entry -> { final IlluminaLaneMetrics laneMetric = new IlluminaLaneMetrics(); laneMetric.LANE = entry.getKey().longValue(); laneMetric.CLUSTER_DENSITY = calculateLaneDensityFromTiles(entry.getValue()); diff --git a/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java b/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java index fb8e9cf6c..457fe9f6d 100644 --- a/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java +++ b/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java @@ -184,9 +184,6 @@ "the number available on the machine less NUM_PROCESSORS.") public int NUM_PROCESSORS = 1; - @Option(doc = "Use the (experimental) new converter that current supports CBCLs output from the NovaSeq", optional = true) - public boolean USE_NEW_CONVERTER = false; - private static final Log LOG = Log.getInstance(ExtractIlluminaBarcodes.class); /** @@ -240,7 +237,7 @@ protected int doWork() { final List extractors = new ArrayList<>(factory.getAvailableTiles().size()); - if (USE_NEW_CONVERTER) { + if (IlluminaFileUtil.hasCbcls(BASECALLS_DIR, LANE)) { final File laneDir = new File(BASECALLS_DIR, IlluminaFileUtil.longLaneStr(LANE)); final File[] cycleDirs = IOUtil.getFilesMatchingRegexp(laneDir, IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN); @@ -445,7 +442,7 @@ private File getBarcodeFile(final int tile) { final IlluminaDataType[] datatypes = (MINIMUM_BASE_QUALITY > 0) ? new IlluminaDataType[]{IlluminaDataType.BaseCalls, IlluminaDataType.PF, IlluminaDataType.QualityScores} : new IlluminaDataType[]{IlluminaDataType.BaseCalls, IlluminaDataType.PF}; - if (USE_NEW_CONVERTER) { + if (IlluminaFileUtil.hasCbcls(BASECALLS_DIR, LANE)) { factory = new IlluminaDataProviderFactory(BASECALLS_DIR, OUTPUT_DIR, LANE, readStructure, bclQualityEvaluationStrategy); } else { factory = new IlluminaDataProviderFactory(BASECALLS_DIR, LANE, readStructure, bclQualityEvaluationStrategy, datatypes); diff --git a/src/main/java/picard/illumina/IlluminaBasecallsConverter.java b/src/main/java/picard/illumina/IlluminaBasecallsConverter.java index bdb650c74..42554c965 100644 --- a/src/main/java/picard/illumina/IlluminaBasecallsConverter.java +++ b/src/main/java/picard/illumina/IlluminaBasecallsConverter.java @@ -66,6 +66,8 @@ * @param The class to which a ClusterData is converted in preparation for writing. */ public class IlluminaBasecallsConverter extends BasecallsConverter { + final boolean includeNonPfReads; + /** * 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 @@ -162,7 +164,7 @@ public IlluminaBasecallsConverter(final File basecallsDir, final int lane, final * @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, + public IlluminaBasecallsConverter(final File basecallsDir, final File barcodesDir, final int lane, final ReadStructure readStructure, final Map> barcodeRecordWriterMap, final boolean demultiplex, @@ -178,10 +180,11 @@ public IlluminaBasecallsConverter(final File basecallsDir, File barcodesDir, fin final boolean ignoreUnexpectedBarcodes ) { super(barcodeRecordWriterMap, maxReadsInRamPerTile, tmpDirs, codecPrototype, ignoreUnexpectedBarcodes, - demultiplex, outputRecordComparator, includeNonPfReads, bclQualityEvaluationStrategy, outputRecordClass, + demultiplex, outputRecordComparator, bclQualityEvaluationStrategy, outputRecordClass, numProcessors, new IlluminaDataProviderFactory(basecallsDir, barcodesDir, lane, readStructure, bclQualityEvaluationStrategy, getDataTypesFromReadStructure(readStructure, demultiplex))); + this.includeNonPfReads = includeNonPfReads; 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. diff --git a/src/main/java/picard/illumina/IlluminaBasecallsToFastq.java b/src/main/java/picard/illumina/IlluminaBasecallsToFastq.java index ecc7f61f4..d538fc9d6 100644 --- a/src/main/java/picard/illumina/IlluminaBasecallsToFastq.java +++ b/src/main/java/picard/illumina/IlluminaBasecallsToFastq.java @@ -45,6 +45,7 @@ import picard.fastq.IlluminaReadNameEncoder; import picard.fastq.ReadNameEncoder; import picard.illumina.parser.ClusterData; +import picard.illumina.parser.IlluminaFileUtil; import picard.illumina.parser.ReadData; import picard.illumina.parser.ReadStructure; import picard.illumina.parser.readers.BclQualityEvaluationStrategy; @@ -196,9 +197,6 @@ @Option(shortName = "GZIP", doc = "Compress output FASTQ files using gzip and append a .gz extension to the file names.") public boolean COMPRESS_OUTPUTS = false; - @Option(doc = "Use the new converter", optional = true) - public boolean USE_NEW_CONVERTER = false; - /** * Simple switch to control the read name format to emit. */ @@ -272,7 +270,7 @@ private void initialize() { demultiplex = true; } final int readsPerCluster = readStructure.templates.length() + readStructure.sampleBarcodes.length(); - if (USE_NEW_CONVERTER) { + if (IlluminaFileUtil.hasCbcls(BASECALLS_DIR, LANE)) { if (BARCODES_DIR == null) BARCODES_DIR = BASECALLS_DIR; basecallsConverter = new NewIlluminaBasecallsConverter<>(BASECALLS_DIR, BARCODES_DIR, LANE, readStructure, sampleBarcodeFastqWriterMap, demultiplex, Math.max(1, MAX_READS_IN_RAM_PER_TILE / readsPerCluster), @@ -280,8 +278,7 @@ private void initialize() { 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); + FastqRecordsForCluster.class, bclQualityEvaluationStrategy, IGNORE_UNEXPECTED_BARCODES); } 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, @@ -298,6 +295,7 @@ private void initialize() { log.info("READ STRUCTURE IS " + readStructure.toString()); } + /** * Assert that expectedCols are present * diff --git a/src/main/java/picard/illumina/IlluminaBasecallsToSam.java b/src/main/java/picard/illumina/IlluminaBasecallsToSam.java index 7b27fdb78..1483f5bbd 100644 --- a/src/main/java/picard/illumina/IlluminaBasecallsToSam.java +++ b/src/main/java/picard/illumina/IlluminaBasecallsToSam.java @@ -43,6 +43,7 @@ import picard.cmdline.Option; import picard.cmdline.StandardOptionDefinitions; import picard.cmdline.programgroups.Illumina; +import picard.illumina.parser.IlluminaFileUtil; import picard.illumina.parser.ReadStructure; import picard.illumina.parser.readers.BclQualityEvaluationStrategy; import picard.util.AdapterPair; @@ -253,9 +254,6 @@ @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; - @Option(doc = "Use the new converter", optional = true) - public boolean USE_NEW_CONVERTER = false; - private final Map barcodeSamWriterMap = new HashMap<>(); private ReadStructure readStructure; private BasecallsConverter basecallsConverter; @@ -272,7 +270,7 @@ protected int doWork() { * Prepares loggers, initiates garbage collection thread, parses arguments and initialized variables appropriately/ */ private void initialize() { - BclQualityEvaluationStrategy bclQualityEvaluationStrategy = new BclQualityEvaluationStrategy(MINIMUM_QUALITY); + final BclQualityEvaluationStrategy bclQualityEvaluationStrategy = new BclQualityEvaluationStrategy(MINIMUM_QUALITY); if (OUTPUT != null) { IOUtil.assertFileIsWritable(OUTPUT); @@ -283,7 +281,7 @@ private void initialize() { } if (OUTPUT != null) { - barcodeSamWriterMap.put(null, buildSamFileWriter(OUTPUT, SAMPLE_ALIAS, LIBRARY_NAME, buildSamHeaderParameters(null), !USE_NEW_CONVERTER)); + barcodeSamWriterMap.put(null, buildSamFileWriter(OUTPUT, SAMPLE_ALIAS, LIBRARY_NAME, buildSamHeaderParameters(null), true)); } else { populateWritersFromLibraryParams(); } @@ -296,15 +294,14 @@ private void initialize() { adapters.add(new CustomAdapterPair(FIVE_PRIME_ADAPTER, THREE_PRIME_ADAPTER)); } - if (USE_NEW_CONVERTER) { + if (IlluminaFileUtil.hasCbcls(BASECALLS_DIR, LANE)) { if (BARCODES_DIR == null) BARCODES_DIR = BASECALLS_DIR; 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, - APPLY_EAMSS_FILTER, INCLUDE_NON_PF_READS, IGNORE_UNEXPECTED_BARCODES); + SAMRecordsForCluster.class, bclQualityEvaluationStrategy, IGNORE_UNEXPECTED_BARCODES); } 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, @@ -420,7 +417,7 @@ private void populateWritersFromLibraryParams() { } final SAMFileWriterWrapper writer = buildSamFileWriter(new File(row.getField("OUTPUT")), - row.getField("SAMPLE_ALIAS"), row.getField("LIBRARY_NAME"), samHeaderParams, !USE_NEW_CONVERTER); + row.getField("SAMPLE_ALIAS"), row.getField("LIBRARY_NAME"), samHeaderParams, true); barcodeSamWriterMap.put(key, writer); } if (barcodeSamWriterMap.isEmpty()) { diff --git a/src/main/java/picard/illumina/IlluminaPhasingMetrics.java b/src/main/java/picard/illumina/IlluminaPhasingMetrics.java index 56c939119..97f4c2a7c 100644 --- a/src/main/java/picard/illumina/IlluminaPhasingMetrics.java +++ b/src/main/java/picard/illumina/IlluminaPhasingMetrics.java @@ -50,7 +50,7 @@ /** 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, boolean usePercentage) { + public static Collection getPhasingMetricsForTiles(final long lane, final Collection tilesForLane, final boolean usePercentage) { final LanePhasingMetricsCollector lanePhasingMetricsCollector = new LanePhasingMetricsCollector(tilesForLane, usePercentage); final Collection phasingMetrics = new ArrayList(); for (final TileTemplateRead tileTemplateRead : lanePhasingMetricsCollector.getMedianPhasingMap().keySet()) { diff --git a/src/main/java/picard/illumina/LanePhasingMetricsCollector.java b/src/main/java/picard/illumina/LanePhasingMetricsCollector.java index c755933a9..ad6f7bcf9 100644 --- a/src/main/java/picard/illumina/LanePhasingMetricsCollector.java +++ b/src/main/java/picard/illumina/LanePhasingMetricsCollector.java @@ -42,7 +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, boolean usePercentage) { + public LanePhasingMetricsCollector(final Collection laneTiles, final boolean usePercentage) { final Map medianPhasingMap = new TreeMap(); final Map medianPrePhasingMap = new TreeMap(); diff --git a/src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java b/src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java index 2c3b968e8..14bff86b7 100644 --- a/src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java +++ b/src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java @@ -55,7 +55,6 @@ * @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, */ public NewIlluminaBasecallsConverter(final File basecallsDir, final File barcodesDir, final int lane, @@ -70,11 +69,10 @@ public NewIlluminaBasecallsConverter(final File basecallsDir, final File barcode final SortingCollection.Codec codecPrototype, final Class outputRecordClass, final BclQualityEvaluationStrategy bclQualityEvaluationStrategy, - final boolean applyEamssFiltering, final boolean includeNonPfReads, final boolean ignoreUnexpectedBarcodes) { super(barcodeRecordWriterMap, maxReadsInRamPerTile, tmpDirs, codecPrototype, ignoreUnexpectedBarcodes, - demultiplex, outputRecordComparator, includeNonPfReads, bclQualityEvaluationStrategy, + demultiplex, outputRecordComparator, bclQualityEvaluationStrategy, outputRecordClass, numProcessors, new IlluminaDataProviderFactory(basecallsDir, barcodesDir, lane, readStructure, bclQualityEvaluationStrategy)); this.tiles = new ArrayList<>(); @@ -137,7 +135,6 @@ public NewIlluminaBasecallsConverter(final File basecallsDir, final File barcode } } - this.factory.setApplyEamssFiltering(applyEamssFiltering); setTileLimits(firstTile, tileLimit); } diff --git a/src/main/java/picard/illumina/parser/IlluminaFileUtil.java b/src/main/java/picard/illumina/parser/IlluminaFileUtil.java index 4fd65def0..b0d83cfa7 100644 --- a/src/main/java/picard/illumina/parser/IlluminaFileUtil.java +++ b/src/main/java/picard/illumina/parser/IlluminaFileUtil.java @@ -36,6 +36,7 @@ import java.io.File; import java.util.ArrayList; +import java.util.Arrays; import java.util.EnumMap; import java.util.Iterator; import java.util.List; @@ -83,7 +84,7 @@ public IlluminaFileUtil(final File basecallDir, final int lane) { } - public IlluminaFileUtil(final File basecallDir, File barcodeDir, final int lane) { + public IlluminaFileUtil(final File basecallDir, final File barcodeDir, final int lane) { this.lane = lane; this.basecallDir = basecallDir; this.barcodeDir = barcodeDir; @@ -221,11 +222,11 @@ public File tileMetricsOut() { * @return A long string representation of the name */ public static String longLaneStr(final int lane) { - String lstr = String.valueOf(lane); + final StringBuilder lstr = new StringBuilder(String.valueOf(lane)); final int zerosToAdd = 3 - lstr.length(); for (int i = 0; i < zerosToAdd; i++) { - lstr = "0" + lstr; + lstr.insert(0, "0"); } return "L" + lstr; } @@ -236,27 +237,41 @@ private String liToStr(final List intList) { return ""; } - String summary = String.valueOf(intList.get(0)); + final StringBuilder summary = new StringBuilder(String.valueOf(intList.get(0))); for (int i = 1; i < intList.size(); i++) { - summary += ", " + String.valueOf(intList.get(i)); + summary.append(", ").append(String.valueOf(intList.get(i))); } - return summary; + return summary.toString(); } private String summarizeTileCounts(final List formats) { - String summary; + final StringBuilder summary; ParameterizedFileUtil pfu = getUtil(formats.get(0)); List tiles = pfu.getTiles(); - summary = pfu.extension + "(" + liToStr(tiles) + ")"; + summary = new StringBuilder(pfu.extension + "(" + liToStr(tiles) + ")"); for (final SupportedIlluminaFormat format : formats) { pfu = getUtil(format); tiles = pfu.getTiles(); - summary += ", " + pfu.extension + "(" + liToStr(tiles) + ")"; + summary.append(", ").append(pfu.extension).append("(").append(liToStr(tiles)).append(")"); } - return summary; + return summary.toString(); + } + + public static boolean hasCbcls(final File basecallDir, final int lane) { + final File laneDir = new File(basecallDir, IlluminaFileUtil.longLaneStr(lane)); + final File[] cycleDirs = IOUtil.getFilesMatchingRegexp(laneDir, IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN); + + //CBCLs + final List cbcls = new ArrayList<>(); + Arrays.asList(cycleDirs) + .forEach(cycleDir -> cbcls.addAll( + Arrays.asList(IOUtil.getFilesMatchingRegexp( + cycleDir, "^" + IlluminaFileUtil.longLaneStr(lane) + "_(\\d{1,5}).cbcl$")))); + + return cbcls.size() > 0; } } diff --git a/src/main/java/picard/illumina/parser/readers/CbclReader.java b/src/main/java/picard/illumina/parser/readers/CbclReader.java index a8f87e7c7..54f32a26a 100644 --- a/src/main/java/picard/illumina/parser/readers/CbclReader.java +++ b/src/main/java/picard/illumina/parser/readers/CbclReader.java @@ -85,6 +85,9 @@ public CbclReader(final List cbcls, final Map filterFileMap, final int[] outputLengths, final int tileNum, final List locs, final int[] outputCycles, final boolean headerOnly) { super(outputLengths); + if (!filterFileMap.containsKey(tileNum)) { + throw new PicardException("Filter file for tile " + tileNum + " does not exist."); + } this.outputCycles = outputCycles; surfaceToTileToCbclMap = sortCbcls(cbcls); diff --git a/src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java b/src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java index 67901e558..bb59bce5b 100644 --- a/src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java +++ b/src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java @@ -50,10 +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 TEST_DATA_DIR_WITH_CBCLS = new File("testdata/picard/illumina/151T8B8B151T_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"); + private static final File DUAL_CBCL_TEST_DATA_DIR = new File("testdata/picard/illumina/151T8B8B151T_cbcl/fastq"); public String getCommandLineProgramName() { return IlluminaBasecallsToFastq.class.getSimpleName(); @@ -140,55 +140,7 @@ public void testDualBarcodes() throws Exception { @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" - }); - - 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); - } + runStandardTest(1, "dualBarcode.", "barcode_double.params", 2, "151T8B8B151T", TEST_DATA_DIR_WITH_CBCLS, DUAL_CBCL_TEST_DATA_DIR); } private void compareFastqs(File testDataDir, File outputSam, String filename) { diff --git a/src/test/java/picard/illumina/IlluminaBasecallsToSamTest.java b/src/test/java/picard/illumina/IlluminaBasecallsToSamTest.java index f7a0d6a2f..108b696bb 100644 --- a/src/test/java/picard/illumina/IlluminaBasecallsToSamTest.java +++ b/src/test/java/picard/illumina/IlluminaBasecallsToSamTest.java @@ -52,8 +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"); + private static final File TEST_DATA_DIR_WITH_CBCLS = new File("testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls"); + private static final File DUAL_CBCL_TEST_DATA_DIR = new File("testdata/picard/illumina/151T8B8B151T_cbcl/sams"); public String getCommandLineProgramName() { return IlluminaBasecallsToSam.class.getSimpleName(); @@ -256,52 +256,9 @@ public void testDualBarcodes() throws Exception { @Test public void testCbclConvert() throws Exception { - runNewConverterTest(1, "dualBarcode.", "barcode_double.params", 2, "151T8B8B151T", TEST_DATA_DIR_WITH_CBCLS, DUAL_CBCL_TEST_DATA_DIR); + runStandardTest(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/parser/readers/CbclReaderTest.java b/src/test/java/picard/illumina/parser/readers/CbclReaderTest.java index 850a0ace3..028b13eb1 100644 --- a/src/test/java/picard/illumina/parser/readers/CbclReaderTest.java +++ b/src/test/java/picard/illumina/parser/readers/CbclReaderTest.java @@ -2,6 +2,7 @@ import org.testng.Assert; import org.testng.annotations.Test; +import picard.PicardException; import picard.illumina.parser.BclData; import java.io.File; @@ -12,25 +13,26 @@ public class CbclReaderTest { - public static final File TestDataDir = new File("testdata/picard/illumina/readerTests/cbcls"); - public static final File PASSING_CBCL_C1_1 = new File(TestDataDir + "/C1.1", "L001_1.cbcl"); - public static final File PASSING_CBCL_C2_1 = new File(TestDataDir + "/C2.1", "L001_1.cbcl"); - public static final File TILE_1101_FILTER = new File(TestDataDir, "tile_1101.filter"); + private static final File TestDataDir = new File("testdata/picard/illumina/readerTests/cbcls"); + private static final File PASSING_CBCL_C1_1 = new File(TestDataDir + "/C1.1", "L001_1.cbcl"); + private static final File PASSING_CBCL_C2_1 = new File(TestDataDir + "/C2.1", "L001_1.cbcl"); + private static final File TILE_1101_FILTER = new File(TestDataDir, "tile_1101.filter"); + private static final File TILE_1102_FILTER = new File(TestDataDir, "tile_1102.filter"); - public static final char[] expectedBases = new char[]{ + private static final char[] expectedBases = new char[]{ 'G', 'G', 'C', 'C', 'G', 'A', 'A', 'G' }; - public static final int[] expectedQuals = new int[]{ + private static final int[] expectedQuals = new int[]{ 37, 37, 37, 37, 37, 37, 37, 12 }; @Test public void testReadValidFile() { - Map filters = new HashMap<>(); + final Map filters = new HashMap<>(); filters.put(1101, TILE_1101_FILTER); - LocsFileReader locsFileReader = new LocsFileReader(new File("testdata/picard/illumina/readerTests/s_1_6.locs")); - List locs = locsFileReader.toList(); + final LocsFileReader locsFileReader = new LocsFileReader(new File("testdata/picard/illumina/readerTests/s_1_6.locs")); + final List locs = locsFileReader.toList(); final CbclReader reader = new CbclReader(Arrays.asList(PASSING_CBCL_C1_1, PASSING_CBCL_C2_1), filters, new int[]{2}, 1101, locs, new int[]{1, 2}, false); @@ -39,8 +41,8 @@ public void testReadValidFile() { final BclData bv = reader.next(); 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]}); + final String actual = new String(new byte[]{bv.bases[cluster][cycle]}); + final 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++; @@ -50,4 +52,15 @@ public void testReadValidFile() { Assert.assertEquals(i, expectedBases.length); reader.close(); } + + @Test(expectedExceptions = PicardException.class) + public void testMissingTile() { + final Map filters = new HashMap<>(); + filters.put(1101, TILE_1101_FILTER); + final LocsFileReader locsFileReader = new LocsFileReader(new File("testdata/picard/illumina/readerTests/s_1_6.locs")); + List locs = locsFileReader.toList(); + new CbclReader(Arrays.asList(PASSING_CBCL_C1_1, PASSING_CBCL_C2_1), + filters, new int[]{2}, 1102, locs, new int[]{1, 2}, false); + + } } diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C1.1/L001_1.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C1.1/L001_1.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C1.1/L001_1.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C1.1/L001_1.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C1.1/L001_2.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C1.1/L001_2.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C1.1/L001_2.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C1.1/L001_2.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C10.1/L001_1.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C10.1/L001_1.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C10.1/L001_1.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C10.1/L001_1.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C10.1/L001_2.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C10.1/L001_2.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C10.1/L001_2.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C10.1/L001_2.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C100.1/L001_1.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C100.1/L001_1.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C100.1/L001_1.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C100.1/L001_1.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C100.1/L001_2.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C100.1/L001_2.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C100.1/L001_2.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C100.1/L001_2.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C101.1/L001_1.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C101.1/L001_1.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C101.1/L001_1.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C101.1/L001_1.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C101.1/L001_2.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C101.1/L001_2.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C101.1/L001_2.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C101.1/L001_2.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C102.1/L001_1.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C102.1/L001_1.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C102.1/L001_1.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C102.1/L001_1.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C102.1/L001_2.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C102.1/L001_2.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C102.1/L001_2.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C102.1/L001_2.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C103.1/L001_1.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C103.1/L001_1.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C103.1/L001_1.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C103.1/L001_1.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C103.1/L001_2.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C103.1/L001_2.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C103.1/L001_2.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C103.1/L001_2.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C104.1/L001_1.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C104.1/L001_1.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C104.1/L001_1.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C104.1/L001_1.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C104.1/L001_2.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C104.1/L001_2.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C104.1/L001_2.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C104.1/L001_2.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C105.1/L001_1.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C105.1/L001_1.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C105.1/L001_1.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C105.1/L001_1.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C105.1/L001_2.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C105.1/L001_2.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C105.1/L001_2.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C105.1/L001_2.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C106.1/L001_1.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C106.1/L001_1.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C106.1/L001_1.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C106.1/L001_1.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C106.1/L001_2.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C106.1/L001_2.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C106.1/L001_2.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C106.1/L001_2.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C107.1/L001_1.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C107.1/L001_1.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C107.1/L001_1.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C107.1/L001_1.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C107.1/L001_2.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C107.1/L001_2.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C107.1/L001_2.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C107.1/L001_2.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C108.1/L001_1.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C108.1/L001_1.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C108.1/L001_1.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C108.1/L001_1.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C108.1/L001_2.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C108.1/L001_2.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C108.1/L001_2.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C108.1/L001_2.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C109.1/L001_1.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C109.1/L001_1.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C109.1/L001_1.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C109.1/L001_1.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C109.1/L001_2.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C109.1/L001_2.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C109.1/L001_2.cbcl rename to testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C109.1/L001_2.cbcl diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C11.1/L001_1.cbcl b/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/L001/C11.1/L001_1.cbcl similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/Data/Intensities/BaseCalls/L001/C11.1/L001_1.cbcl rename to 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a/testdata/picard/illumina/125T8B8B125T_cbcl/sams/CCCCGCTTTTGCGTGT.sam b/testdata/picard/illumina/151T8B8B151T_cbcl/sams/CCCCGCTTTTGCGTGT.sam similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/sams/CCCCGCTTTTGCGTGT.sam rename to testdata/picard/illumina/151T8B8B151T_cbcl/sams/CCCCGCTTTTGCGTGT.sam diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/sams/GCTATAGTCCAGCAGC.sam b/testdata/picard/illumina/151T8B8B151T_cbcl/sams/GCTATAGTCCAGCAGC.sam similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/sams/GCTATAGTCCAGCAGC.sam rename to testdata/picard/illumina/151T8B8B151T_cbcl/sams/GCTATAGTCCAGCAGC.sam diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/sams/NN.sam b/testdata/picard/illumina/151T8B8B151T_cbcl/sams/NN.sam similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/sams/NN.sam rename to testdata/picard/illumina/151T8B8B151T_cbcl/sams/NN.sam diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/sams/TTGCGGCCGGTTTAAC.sam b/testdata/picard/illumina/151T8B8B151T_cbcl/sams/TTGCGGCCGGTTTAAC.sam similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/sams/TTGCGGCCGGTTTAAC.sam rename to testdata/picard/illumina/151T8B8B151T_cbcl/sams/TTGCGGCCGGTTTAAC.sam diff --git a/testdata/picard/illumina/125T8B8B125T_cbcl/sams/barcode_double.params b/testdata/picard/illumina/151T8B8B151T_cbcl/sams/barcode_double.params similarity index 100% rename from testdata/picard/illumina/125T8B8B125T_cbcl/sams/barcode_double.params rename to testdata/picard/illumina/151T8B8B151T_cbcl/sams/barcode_double.params From df6f8399c2df5b685d00cea85cd565747c7ca338 Mon Sep 17 00:00:00 2001 From: jacarey Date: Thu, 29 Jun 2017 09:01:20 -0400 Subject: [PATCH 6/6] A few more review changes. --- .../java/picard/illumina/CollectIlluminaBasecallingMetrics.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java b/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java index 092284e22..def1caeca 100644 --- a/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java +++ b/src/main/java/picard/illumina/CollectIlluminaBasecallingMetrics.java @@ -129,7 +129,7 @@ public File OUTPUT; private int barcodeLength = 0; - private String unmatched_barcode; + private String unmatchedBarcode; private final SortedMap barcodeToMetricCounts; private static final String BARCODE_NAME_COLUMN = "barcode_name"; @@ -196,7 +196,7 @@ protected int doWork() { } } - unmatched_barcode = StringUtil.repeatCharNTimes('N', barcodeLength); + unmatchedBarcode = StringUtil.repeatCharNTimes('N', barcodeLength); //Initialize data provider, iterate over clusters, and collect statistics if (IlluminaFileUtil.hasCbcls(BASECALLS_DIR, LANE)) { @@ -251,10 +251,10 @@ private void setupNewDataProvider(final IlluminaDataProviderFactory factory) { final Map barcodesFiles = new HashMap<>(); - IOUtil.assertFilesAreReadable(new ArrayList<>(barcodesFiles.values())); for (final File barcodeFile : NewIlluminaBasecallsConverter.getTiledFiles(laneDir, barcodeRegex)) { final Matcher tileMatcher = barcodeRegex.matcher(barcodeFile.getName()); if (tileMatcher.matches()) { + IOUtil.assertFileIsReadable(barcodeFile); barcodesFiles.put(Integer.valueOf(tileMatcher.group(1)), barcodeFile); } } @@ -274,7 +274,7 @@ private void setupNewDataProvider(final IlluminaDataProviderFactory factory) { private void addCluster(final ClusterData cluster) { //compute hash of Barcode and Lane for key String barcode = cluster.getMatchedBarcode(); - if (barcode == null) barcode = unmatched_barcode; + if (barcode == null) barcode = unmatchedBarcode; //increment counts IlluminaMetricCounts counters = barcodeToMetricCounts.get(barcode);