diff --git a/src/main/java/picard/analysis/CollectGcBiasMetrics.java b/src/main/java/picard/analysis/CollectGcBiasMetrics.java index 30ed75677..4f75493d6 100644 --- a/src/main/java/picard/analysis/CollectGcBiasMetrics.java +++ b/src/main/java/picard/analysis/CollectGcBiasMetrics.java @@ -34,7 +34,6 @@ import picard.cmdline.Option; import picard.cmdline.programgroups.Metrics; import picard.metrics.GcBiasMetrics; -import picard.metrics.MultiLevelCollector; import picard.util.RExecutor; import java.io.File; diff --git a/src/main/java/picard/analysis/CollectOxoGMetrics.java b/src/main/java/picard/analysis/CollectOxoGMetrics.java index ae3c10103..468bb35bf 100644 --- a/src/main/java/picard/analysis/CollectOxoGMetrics.java +++ b/src/main/java/picard/analysis/CollectOxoGMetrics.java @@ -468,7 +468,7 @@ private Counts computeAlleleFraction(final SamLocusIterator.LocusInfo info, fina final Counts counts = new Counts(); final byte altBase = (refBase == 'C') ? (byte) 'A' : (byte) 'T'; - for (final SamLocusIterator.RecordAndOffset rec : info.getRecordAndPositions()) { + for (final SamLocusIterator.RecordAndOffset rec : info.getRecordAndOffsets()) { final byte qual; final SAMRecord samrec = rec.getRecord(); diff --git a/src/main/java/picard/analysis/CollectQualityYieldMetrics.java b/src/main/java/picard/analysis/CollectQualityYieldMetrics.java index f3d16f625..a704bfb89 100644 --- a/src/main/java/picard/analysis/CollectQualityYieldMetrics.java +++ b/src/main/java/picard/analysis/CollectQualityYieldMetrics.java @@ -26,15 +26,10 @@ import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMRecord; -import htsjdk.samtools.SamReader; -import htsjdk.samtools.SamReaderFactory; import htsjdk.samtools.metrics.MetricBase; import htsjdk.samtools.metrics.MetricsFile; import htsjdk.samtools.reference.ReferenceSequence; import htsjdk.samtools.util.IOUtil; -import htsjdk.samtools.util.Log; -import htsjdk.samtools.util.ProgressLogger; -import picard.cmdline.CommandLineProgram; import picard.cmdline.CommandLineProgramProperties; import picard.cmdline.Option; import picard.cmdline.StandardOptionDefinitions; diff --git a/src/main/java/picard/analysis/CollectWgsMetrics.java b/src/main/java/picard/analysis/CollectWgsMetrics.java index a52dc42ef..ab7df819f 100644 --- a/src/main/java/picard/analysis/CollectWgsMetrics.java +++ b/src/main/java/picard/analysis/CollectWgsMetrics.java @@ -639,11 +639,11 @@ public WgsMetricsCollector(final int coverageCap, final IntervalList intervals) public void addInfo(final SamLocusIterator.LocusInfo info) { // Figure out the coverage while not counting overlapping reads twice, and excluding various things - final HashSet readNames = new HashSet<>(info.getRecordAndPositions().size()); + final HashSet readNames = new HashSet<>(info.getRecordAndOffsets().size()); int pileupSize = 0; int unfilteredDepth = 0; - for (final SamLocusIterator.RecordAndOffset recs : info.getRecordAndPositions()) { + for (final SamLocusIterator.RecordAndOffset recs : info.getRecordAndOffsets()) { if (recs.getBaseQuality() <= 2) { ++basesExcludedByBaseq; continue; } // we add to the base quality histogram any bases that have quality > 2 diff --git a/src/main/java/picard/analysis/JumpingLibraryMetrics.java b/src/main/java/picard/analysis/JumpingLibraryMetrics.java index 4e2e62c63..9e28b6c97 100644 --- a/src/main/java/picard/analysis/JumpingLibraryMetrics.java +++ b/src/main/java/picard/analysis/JumpingLibraryMetrics.java @@ -23,8 +23,6 @@ */ package picard.analysis; -import picard.sam.DuplicationMetrics; -import htsjdk.samtools.util.Histogram; import htsjdk.samtools.metrics.MetricBase; /** diff --git a/src/main/java/picard/analysis/artifacts/SequencingArtifactMetrics.java b/src/main/java/picard/analysis/artifacts/SequencingArtifactMetrics.java index 12c9a23c9..8d3b0e3c7 100644 --- a/src/main/java/picard/analysis/artifacts/SequencingArtifactMetrics.java +++ b/src/main/java/picard/analysis/artifacts/SequencingArtifactMetrics.java @@ -3,8 +3,6 @@ import htsjdk.samtools.metrics.MetricBase; import htsjdk.samtools.util.QualityUtil; -import java.util.Comparator; - public class SequencingArtifactMetrics { public static final String PRE_ADAPTER_SUMMARY_EXT = ".pre_adapter_summary_metrics"; public static final String PRE_ADAPTER_DETAILS_EXT = ".pre_adapter_detail_metrics"; diff --git a/src/main/java/picard/analysis/directed/CollectTargetedMetrics.java b/src/main/java/picard/analysis/directed/CollectTargetedMetrics.java index 9b350033a..2ec89d370 100644 --- a/src/main/java/picard/analysis/directed/CollectTargetedMetrics.java +++ b/src/main/java/picard/analysis/directed/CollectTargetedMetrics.java @@ -2,7 +2,6 @@ import htsjdk.samtools.SAMReadGroupRecord; import htsjdk.samtools.SAMRecord; -import htsjdk.samtools.SAMRecordIterator; import htsjdk.samtools.SamReader; import htsjdk.samtools.SamReaderFactory; import htsjdk.samtools.metrics.MetricsFile; diff --git a/src/main/java/picard/analysis/directed/InsertSizeMetricsCollector.java b/src/main/java/picard/analysis/directed/InsertSizeMetricsCollector.java index d278ae88d..063cbf3f8 100644 --- a/src/main/java/picard/analysis/directed/InsertSizeMetricsCollector.java +++ b/src/main/java/picard/analysis/directed/InsertSizeMetricsCollector.java @@ -11,7 +11,6 @@ import picard.metrics.MultiLevelCollector; import picard.metrics.PerUnitMetricCollector; -import java.util.Collections; import java.util.EnumMap; import java.util.List; import java.util.Map; diff --git a/src/main/java/picard/analysis/directed/TargetMetricsCollector.java b/src/main/java/picard/analysis/directed/TargetMetricsCollector.java index a822e5023..c5a1fee4e 100644 --- a/src/main/java/picard/analysis/directed/TargetMetricsCollector.java +++ b/src/main/java/picard/analysis/directed/TargetMetricsCollector.java @@ -310,7 +310,7 @@ public TargetMetricsCollector(final Set accumulationLev if (refFile != null) { intervalToGc = new HashMap(); for (final Interval target : uniqueTargets) { - final ReferenceSequence rs = refFile.getSubsequenceAt(target.getSequence(), target.getStart(), target.getEnd()); + final ReferenceSequence rs = refFile.getSubsequenceAt(target.getContig(), target.getStart(), target.getEnd()); intervalToGc.put(target,SequenceUtil.calculateGc(rs.getBases())); } } @@ -798,7 +798,7 @@ private void calculateGcMetrics() { if (max < d) max = d; } - out.println(interval.getSequence() + "\t" + + out.println(interval.getContig() + "\t" + interval.getStart() + "\t" + interval.getEnd() + "\t" + interval.length() + "\t" + diff --git a/src/main/java/picard/cmdline/CommandLineParser.java b/src/main/java/picard/cmdline/CommandLineParser.java index eb2732f24..9a72f1586 100644 --- a/src/main/java/picard/cmdline/CommandLineParser.java +++ b/src/main/java/picard/cmdline/CommandLineParser.java @@ -50,7 +50,6 @@ import java.util.List; import java.util.Map; import java.util.Set; -import java.util.regex.Matcher; import java.util.regex.Pattern; /** diff --git a/src/main/java/picard/cmdline/CommandLineProgram.java b/src/main/java/picard/cmdline/CommandLineProgram.java index 02a59654e..1fe82f215 100644 --- a/src/main/java/picard/cmdline/CommandLineProgram.java +++ b/src/main/java/picard/cmdline/CommandLineProgram.java @@ -36,13 +36,10 @@ import htsjdk.samtools.util.BlockCompressedStreamConstants; import htsjdk.samtools.util.IOUtil; import htsjdk.samtools.util.Log; -import htsjdk.samtools.util.zip.DeflaterFactory; import htsjdk.variant.variantcontext.writer.Options; import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; import java.io.File; -import java.lang.annotation.Annotation; -import java.lang.reflect.Field; import java.net.InetAddress; import java.text.DecimalFormat; import java.util.ArrayList; diff --git a/src/main/java/picard/cmdline/PicardCommandLine.java b/src/main/java/picard/cmdline/PicardCommandLine.java index c35198c47..771a4aaef 100644 --- a/src/main/java/picard/cmdline/PicardCommandLine.java +++ b/src/main/java/picard/cmdline/PicardCommandLine.java @@ -1,6 +1,5 @@ package picard.cmdline; -import htsjdk.samtools.Defaults; import htsjdk.samtools.util.Log; import htsjdk.samtools.util.StringUtil; diff --git a/src/main/java/picard/fastq/BamToBfqWriter.java b/src/main/java/picard/fastq/BamToBfqWriter.java index 04dd5d3a2..d0d908c26 100644 --- a/src/main/java/picard/fastq/BamToBfqWriter.java +++ b/src/main/java/picard/fastq/BamToBfqWriter.java @@ -30,7 +30,7 @@ import htsjdk.samtools.SamReaderFactory; import htsjdk.samtools.filter.AggregateFilter; import htsjdk.samtools.filter.FailsVendorReadQualityFilter; -import htsjdk.samtools.filter.FilteringIterator; +import htsjdk.samtools.filter.FilteringSamIterator; import htsjdk.samtools.filter.SamRecordFilter; import htsjdk.samtools.filter.TagFilter; import htsjdk.samtools.filter.WholeReadClippedFilter; @@ -236,7 +236,7 @@ private void writeSingleEndBfqs(final Iterator iterator, final List fingerprints final HaplotypeBlock haplotypeBlock = this.haplotypes.getHaplotype(info.getSequenceName(), info.getPosition()); final Snp snp = this.haplotypes.getSnp(info.getSequenceName(), info.getPosition()); - for (final SamLocusIterator.RecordAndOffset rec : info.getRecordAndPositions()) { + for (final SamLocusIterator.RecordAndOffset rec : info.getRecordAndOffsets()) { final SAMReadGroupRecord rg = rec.getRecord().getReadGroup(); if (rg == null || !fingerprintsByReadGroup.containsKey(rg)) { final PicardException e = new PicardException("Unknown read group: " + rg); @@ -390,7 +390,7 @@ public IntervalList getLociToGenotype(final Collection fingerprints final Snp snp = this.haplotypes.getSnp(info.getSequenceName(), info.getPosition()); // randomly select locusMaxReads elements from the list - final List recordAndOffsetList = randomSublist(info.getRecordAndPositions(), locusMaxReads); + final List recordAndOffsetList = randomSublist(info.getRecordAndOffsets(), locusMaxReads); for (final SamLocusIterator.RecordAndOffset rec : recordAndOffsetList) { final SAMReadGroupRecord rg = rec.getRecord().getReadGroup(); diff --git a/src/main/java/picard/fingerprint/GenotypeReader.java b/src/main/java/picard/fingerprint/GenotypeReader.java index e9c4248f0..564aea5bf 100644 --- a/src/main/java/picard/fingerprint/GenotypeReader.java +++ b/src/main/java/picard/fingerprint/GenotypeReader.java @@ -24,6 +24,7 @@ package picard.fingerprint; +import htsjdk.tribble.readers.SynchronousLineReader; import picard.PicardException; import htsjdk.samtools.util.IOUtil; import htsjdk.samtools.util.Interval; @@ -33,7 +34,6 @@ import htsjdk.samtools.util.CloseableIterator; import htsjdk.tribble.readers.LineIterator; import htsjdk.tribble.readers.LineIteratorImpl; -import htsjdk.tribble.readers.LineReaderUtil; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFCodec; @@ -140,7 +140,7 @@ boolean isVcf(final File f) { * @deprecated Please use VCFFileReader in Picard-public instead of this class. */ VariantIterator readVcf(final File file) { - final LineIterator reader = new LineIteratorImpl(LineReaderUtil.fromBufferedStream(new BufferedInputStream(IOUtil.openFileForReading(file)))); + final LineIterator reader = new LineIteratorImpl(new SynchronousLineReader(new BufferedInputStream(IOUtil.openFileForReading(file)))); final VCFCodec codec = new VCFCodec(); final Object header; header = codec.readActualHeader(reader); diff --git a/src/main/java/picard/fingerprint/HaplotypeMap.java b/src/main/java/picard/fingerprint/HaplotypeMap.java index fe3fd57fb..50ea20818 100644 --- a/src/main/java/picard/fingerprint/HaplotypeMap.java +++ b/src/main/java/picard/fingerprint/HaplotypeMap.java @@ -49,7 +49,7 @@ private final Map haplotypesBySnpName = new HashMap(); private final Map haplotypesBySnpLocus = new HashMap(); private final Map snpsByPosition = new HashMap(); - private final IntervalList intervals; + private IntervalList intervals; private final SAMFileHeader header; /** @@ -207,7 +207,7 @@ public Snp getSnp(final String chrom, final int pos) { /** Returns an IntervalList with an entry for every SNP in every Haplotype in the map. */ public IntervalList getIntervalList() { - this.intervals.sort(); // TODO: should probably do this elsewhere + this.intervals = this.intervals.sorted(); // TODO: should probably do this elsewhere return this.intervals; } diff --git a/src/main/java/picard/illumina/IlluminaBasecallsToSam.java b/src/main/java/picard/illumina/IlluminaBasecallsToSam.java index 5f7859a0f..54aa196a8 100644 --- a/src/main/java/picard/illumina/IlluminaBasecallsToSam.java +++ b/src/main/java/picard/illumina/IlluminaBasecallsToSam.java @@ -44,7 +44,6 @@ import picard.cmdline.programgroups.Illumina; import picard.cmdline.StandardOptionDefinitions; import picard.illumina.parser.ReadStructure; -import picard.illumina.parser.ReadType; import picard.illumina.parser.readers.BclQualityEvaluationStrategy; import picard.util.IlluminaUtil; import picard.util.IlluminaUtil.IlluminaAdapterPair; @@ -55,7 +54,6 @@ import java.io.OutputStream; import java.util.ArrayList; import java.util.Arrays; -import java.util.Collections; import java.util.Comparator; import java.util.Date; import java.util.HashMap; diff --git a/src/main/java/picard/illumina/LanePhasingMetricsCollector.java b/src/main/java/picard/illumina/LanePhasingMetricsCollector.java index ffa65560f..0f542ef95 100644 --- a/src/main/java/picard/illumina/LanePhasingMetricsCollector.java +++ b/src/main/java/picard/illumina/LanePhasingMetricsCollector.java @@ -29,7 +29,11 @@ import picard.util.MathUtil; import htsjdk.samtools.util.CollectionUtil; -import java.lang.Float;import java.util.*;import java.util.Collection;import java.util.Collections;import java.util.Map;import java.util.TreeMap; +import java.lang.Float; +import java.util.Collection; +import java.util.Collections; +import java.util.Map; +import java.util.TreeMap; /** Helper class used to transform tile data for a lane into a collection of IlluminaPhasingMetrics */ public class LanePhasingMetricsCollector { diff --git a/src/main/java/picard/illumina/parser/IlluminaFileUtil.java b/src/main/java/picard/illumina/parser/IlluminaFileUtil.java index 69f92a7f2..736054792 100644 --- a/src/main/java/picard/illumina/parser/IlluminaFileUtil.java +++ b/src/main/java/picard/illumina/parser/IlluminaFileUtil.java @@ -37,7 +37,6 @@ import java.io.File; import java.util.ArrayList; import java.util.EnumMap; -import java.util.HashMap; import java.util.Iterator; import java.util.List; import java.util.Map; diff --git a/src/main/java/picard/illumina/parser/Tile.java b/src/main/java/picard/illumina/parser/Tile.java index 2763003d0..9b3abf769 100644 --- a/src/main/java/picard/illumina/parser/Tile.java +++ b/src/main/java/picard/illumina/parser/Tile.java @@ -30,7 +30,6 @@ import java.util.Collection; import java.util.Collections; import java.util.EnumMap; -import java.util.HashMap; import java.util.LinkedList; import java.util.List; import java.util.Map; diff --git a/src/main/java/picard/illumina/parser/TileMetricsUtil.java b/src/main/java/picard/illumina/parser/TileMetricsUtil.java index 2888d9d44..35863d3b2 100644 --- a/src/main/java/picard/illumina/parser/TileMetricsUtil.java +++ b/src/main/java/picard/illumina/parser/TileMetricsUtil.java @@ -38,7 +38,6 @@ import java.util.HashMap; import java.util.Iterator; import java.util.LinkedList; -import java.util.List; import java.util.Map; import java.util.Set; import java.util.stream.Collectors; diff --git a/src/main/java/picard/reference/ExtractSequences.java b/src/main/java/picard/reference/ExtractSequences.java index 4dc6c0468..aaf3df61d 100644 --- a/src/main/java/picard/reference/ExtractSequences.java +++ b/src/main/java/picard/reference/ExtractSequences.java @@ -98,7 +98,7 @@ protected int doWork() { final BufferedWriter out = IOUtil.openFileForBufferedWriting(OUTPUT); for (final Interval interval : intervals) { - final ReferenceSequence seq = ref.getSubsequenceAt(interval.getSequence(), interval.getStart(), interval.getEnd()); + final ReferenceSequence seq = ref.getSubsequenceAt(interval.getContig(), interval.getStart(), interval.getEnd()); final byte[] bases = seq.getBases(); if (interval.isNegativeStrand()) SequenceUtil.reverseComplement(bases); diff --git a/src/main/java/picard/sam/CreateSequenceDictionary.java b/src/main/java/picard/sam/CreateSequenceDictionary.java index 90774a748..b215c3c2b 100644 --- a/src/main/java/picard/sam/CreateSequenceDictionary.java +++ b/src/main/java/picard/sam/CreateSequenceDictionary.java @@ -52,7 +52,6 @@ import java.util.ArrayList; import java.util.HashSet; import java.util.List; -import java.util.Optional; import java.util.Set; /** diff --git a/src/main/java/picard/sam/FastqToSam.java b/src/main/java/picard/sam/FastqToSam.java index 4d89d8527..ef605ba0b 100644 --- a/src/main/java/picard/sam/FastqToSam.java +++ b/src/main/java/picard/sam/FastqToSam.java @@ -32,7 +32,6 @@ import htsjdk.samtools.SAMReadGroupRecord; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.SAMUtils; -import htsjdk.samtools.fastq.FastqConstants; import htsjdk.samtools.fastq.FastqConstants.FastqExtensions; import htsjdk.samtools.fastq.FastqReader; import htsjdk.samtools.fastq.FastqRecord; diff --git a/src/main/java/picard/sam/MultiHitAlignedReadIterator.java b/src/main/java/picard/sam/MultiHitAlignedReadIterator.java index e1e10acf0..111d8bcec 100644 --- a/src/main/java/picard/sam/MultiHitAlignedReadIterator.java +++ b/src/main/java/picard/sam/MultiHitAlignedReadIterator.java @@ -30,7 +30,7 @@ import htsjdk.samtools.SAMRecordQueryNameComparator; import htsjdk.samtools.SAMTag; import htsjdk.samtools.SAMUtils; -import htsjdk.samtools.filter.FilteringIterator; +import htsjdk.samtools.filter.FilteringSamIterator; import htsjdk.samtools.filter.SamRecordFilter; import htsjdk.samtools.util.CloseableIterator; import htsjdk.samtools.util.PeekableIterator; @@ -70,7 +70,7 @@ MultiHitAlignedReadIterator(final CloseableIterator querynameOrderIterator, final PrimaryAlignmentSelectionStrategy primaryAlignmentSelectionStrategy) { this.primaryAlignmentSelectionStrategy = primaryAlignmentSelectionStrategy; - peekIterator = new PeekableIterator(new FilteringIterator(querynameOrderIterator, + peekIterator = new PeekableIterator(new FilteringSamIterator(querynameOrderIterator, new SamRecordFilter() { // Filter unmapped reads. public boolean filterOut(final SAMRecord record) { diff --git a/src/main/java/picard/sam/ReorderSam.java b/src/main/java/picard/sam/ReorderSam.java index a0714e01f..06175f7f4 100644 --- a/src/main/java/picard/sam/ReorderSam.java +++ b/src/main/java/picard/sam/ReorderSam.java @@ -149,7 +149,7 @@ private int newOrderIndex(SAMRecord read, int oldIndex, Map ne else { final Integer n = newOrder.get(oldIndex); - if (n == null) throw new PicardException("BUG: no mapping found for read " + read.format()); + if (n == null) throw new PicardException("BUG: no mapping found for read " + read.getSAMString()); else return n; } } diff --git a/src/main/java/picard/sam/RevertSam.java b/src/main/java/picard/sam/RevertSam.java index b3b18411f..c567d8920 100644 --- a/src/main/java/picard/sam/RevertSam.java +++ b/src/main/java/picard/sam/RevertSam.java @@ -32,12 +32,11 @@ import htsjdk.samtools.SAMReadGroupRecord; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.SAMRecordQueryNameComparator; -import htsjdk.samtools.SAMRecordUtil; import htsjdk.samtools.SAMTag; import htsjdk.samtools.SamReader; import htsjdk.samtools.SamReaderFactory; import htsjdk.samtools.ValidationStringency; -import htsjdk.samtools.filter.FilteringIterator; +import htsjdk.samtools.filter.FilteringSamIterator; import htsjdk.samtools.filter.SamRecordFilter; import htsjdk.samtools.util.CloserUtil; import htsjdk.samtools.util.FastqQualityFormat; @@ -526,7 +525,7 @@ public boolean filterOut(final SAMRecord first, final SAMRecord second) { throw new UnsupportedOperationException(); } }; - readGroupToFormat.put(rg, QualityEncodingDetector.detect(QualityEncodingDetector.DEFAULT_MAX_RECORDS_TO_ITERATE, new FilteringIterator(reader.iterator(), filter), restoreOriginalQualities)); + readGroupToFormat.put(rg, QualityEncodingDetector.detect(QualityEncodingDetector.DEFAULT_MAX_RECORDS_TO_ITERATE, new FilteringSamIterator(reader.iterator(), filter), restoreOriginalQualities)); CloserUtil.close(reader); } for (final SAMReadGroupRecord r : readGroupToFormat.keySet()) { diff --git a/src/main/java/picard/sam/SamAlignmentMerger.java b/src/main/java/picard/sam/SamAlignmentMerger.java index a716c4bb6..b364b9bdb 100644 --- a/src/main/java/picard/sam/SamAlignmentMerger.java +++ b/src/main/java/picard/sam/SamAlignmentMerger.java @@ -13,10 +13,8 @@ import htsjdk.samtools.SamPairUtil; import htsjdk.samtools.SamReader; import htsjdk.samtools.SamReaderFactory; -import htsjdk.samtools.ValidationStringency; import htsjdk.samtools.filter.OverclippedReadFilter; import htsjdk.samtools.util.CloseableIterator; -import htsjdk.samtools.util.CloserUtil; import htsjdk.samtools.util.DelegatingIterator; import htsjdk.samtools.util.IOUtil; import htsjdk.samtools.util.Log; diff --git a/src/main/java/picard/sam/markduplicates/util/AbstractMarkDuplicatesCommandLineProgram.java b/src/main/java/picard/sam/markduplicates/util/AbstractMarkDuplicatesCommandLineProgram.java index 5bf6972f4..775a771d8 100644 --- a/src/main/java/picard/sam/markduplicates/util/AbstractMarkDuplicatesCommandLineProgram.java +++ b/src/main/java/picard/sam/markduplicates/util/AbstractMarkDuplicatesCommandLineProgram.java @@ -36,7 +36,6 @@ import htsjdk.samtools.metrics.MetricsFile; import htsjdk.samtools.util.CloseableIterator; import htsjdk.samtools.util.Histogram; -import htsjdk.samtools.util.Log; import picard.PicardException; import picard.cmdline.Option; import picard.cmdline.StandardOptionDefinitions; diff --git a/src/main/java/picard/sam/markduplicates/util/ReadEndsForMarkDuplicatesWithBarcodesCodec.java b/src/main/java/picard/sam/markduplicates/util/ReadEndsForMarkDuplicatesWithBarcodesCodec.java index f230a4183..d7caf42b4 100644 --- a/src/main/java/picard/sam/markduplicates/util/ReadEndsForMarkDuplicatesWithBarcodesCodec.java +++ b/src/main/java/picard/sam/markduplicates/util/ReadEndsForMarkDuplicatesWithBarcodesCodec.java @@ -27,7 +27,6 @@ import htsjdk.samtools.util.SortingCollection; import picard.PicardException; -import java.io.EOFException; import java.io.IOException; /** diff --git a/src/main/java/picard/util/BaitDesigner.java b/src/main/java/picard/util/BaitDesigner.java index 895b43fc0..2dbb05584 100644 --- a/src/main/java/picard/util/BaitDesigner.java +++ b/src/main/java/picard/util/BaitDesigner.java @@ -123,7 +123,7 @@ public String toString() { if (target.length() <= baitSize) { final int midpoint = target.getStart() + (target.length() / 2); final int baitStart = midpoint - (baitSize / 2); - final Bait bait = new Bait(target.getSequence(), + final Bait bait = new Bait(target.getContig(), baitStart, CoordMath.getEnd(baitStart, baitSize), target.isNegativeStrand(), @@ -142,7 +142,7 @@ public String toString() { int start = firstBaitStart; while (start <= lastBaitStart) { final int end = CoordMath.getEnd(start, baitSize); - final Bait bait = new Bait(target.getSequence(), + final Bait bait = new Bait(target.getContig(), start, end, target.isNegativeStrand(), @@ -179,7 +179,7 @@ public String toString() { final int addon = minTargetSize - target.length(); final int left = addon / 2; final int right = addon - left; - t2 = new Interval(target.getSequence(), + t2 = new Interval(target.getContig(), Math.max(target.getStart() - left, 1), Math.min(target.getEnd() + right, reference.length()), target.isNegativeStrand(), @@ -223,7 +223,7 @@ public String toString() { } } - final Bait bait = new Bait(t2.getSequence(), + final Bait bait = new Bait(t2.getContig(), start, end, t2.isNegativeStrand(), @@ -251,7 +251,7 @@ public String toString() { int i = 0; for (int start = target.getStart(); start < lastPossibleBaitStart; start += baitOffset) { - final Bait bait = new Bait(target.getSequence(), + final Bait bait = new Bait(target.getContig(), start, CoordMath.getEnd(start, baitSize), target.isNegativeStrand(), @@ -415,9 +415,9 @@ protected int doWork() { final IntervalList padded = new IntervalList(originalTargets.getHeader()); final SAMSequenceDictionary dict = padded.getHeader().getSequenceDictionary(); for (final Interval i : originalTargets.getIntervals()) { - padded.add(new Interval(i.getSequence(), + padded.add(new Interval(i.getContig(), Math.max(i.getStart() - PADDING, 1), - Math.min(i.getEnd() + PADDING, dict.getSequence(i.getSequence()).getSequenceLength()), + Math.min(i.getEnd() + PADDING, dict.getSequence(i.getContig()).getSequenceLength()), i.isNegativeStrand(), i.getName())); } @@ -434,10 +434,10 @@ protected int doWork() { while (iterator.hasNext()) { final Interval next = iterator.next(); - if (previous.getSequence().equals(next.getSequence()) && + if (previous.getContig().equals(next.getContig()) && estimateBaits(previous.getStart(), previous.getEnd()) + estimateBaits(next.getStart(), next.getEnd()) >= estimateBaits(previous.getStart(), next.getEnd())) { - previous = new Interval(previous.getSequence(), + previous = new Interval(previous.getContig(), previous.getStart(), Math.max(previous.getEnd(), next.getEnd()), previous.isNegativeStrand(), @@ -465,7 +465,7 @@ protected int doWork() { int discardedBaits = 0; final IntervalList baits = new IntervalList(targets.getHeader()); for (final Interval target : targets) { - final int sequenceIndex = targets.getHeader().getSequenceIndex(target.getSequence()); + final int sequenceIndex = targets.getHeader().getSequenceIndex(target.getContig()); final ReferenceSequence reference = referenceWalker.get(sequenceIndex); for (final Bait bait : DESIGN_STRATEGY.design(this, target, reference)) { diff --git a/src/main/java/picard/util/BedToIntervalList.java b/src/main/java/picard/util/BedToIntervalList.java index c89371302..886a40e5d 100644 --- a/src/main/java/picard/util/BedToIntervalList.java +++ b/src/main/java/picard/util/BedToIntervalList.java @@ -3,7 +3,6 @@ import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.SAMSequenceRecord; -import htsjdk.samtools.SamReaderFactory; import htsjdk.samtools.util.CloserUtil; import htsjdk.samtools.util.IOUtil; import htsjdk.samtools.util.Interval; diff --git a/src/main/java/picard/util/IntervalListScatterer.java b/src/main/java/picard/util/IntervalListScatterer.java index 125182b44..34afa42c8 100644 --- a/src/main/java/picard/util/IntervalListScatterer.java +++ b/src/main/java/picard/util/IntervalListScatterer.java @@ -2,7 +2,6 @@ import htsjdk.samtools.util.Interval; import htsjdk.samtools.util.IntervalList; -import picard.PicardException; import java.util.ArrayDeque; import java.util.ArrayList; diff --git a/src/main/java/picard/vcf/ByIntervalListVariantContextIterator.java b/src/main/java/picard/vcf/ByIntervalListVariantContextIterator.java index bf79f7b24..54b89f512 100644 --- a/src/main/java/picard/vcf/ByIntervalListVariantContextIterator.java +++ b/src/main/java/picard/vcf/ByIntervalListVariantContextIterator.java @@ -8,9 +8,6 @@ import htsjdk.variant.vcf.VCFFileReader; import java.util.Iterator; -import java.util.NoSuchElementException; -import java.util.Optional; -import java.util.Set; /** * Takes a VCFFileReader and an IntervalList and provides a single iterator over all variants in all the intervals. diff --git a/src/main/java/picard/vcf/GA4GHScheme.java b/src/main/java/picard/vcf/GA4GHScheme.java index 3bd2e91aa..de340c8e3 100644 --- a/src/main/java/picard/vcf/GA4GHScheme.java +++ b/src/main/java/picard/vcf/GA4GHScheme.java @@ -24,7 +24,6 @@ package picard.vcf; -import picard.PicardException; import picard.vcf.GenotypeConcordanceStates.*; /** diff --git a/src/main/java/picard/vcf/GA4GHSchemeWithMissingAsHomRef.java b/src/main/java/picard/vcf/GA4GHSchemeWithMissingAsHomRef.java index c75d91b19..dc5ae4325 100644 --- a/src/main/java/picard/vcf/GA4GHSchemeWithMissingAsHomRef.java +++ b/src/main/java/picard/vcf/GA4GHSchemeWithMissingAsHomRef.java @@ -24,7 +24,6 @@ package picard.vcf; -import picard.PicardException; import picard.vcf.GenotypeConcordanceStates.*; /** diff --git a/src/main/java/picard/vcf/GenotypeConcordanceCounts.java b/src/main/java/picard/vcf/GenotypeConcordanceCounts.java index cef0c3619..31e738636 100644 --- a/src/main/java/picard/vcf/GenotypeConcordanceCounts.java +++ b/src/main/java/picard/vcf/GenotypeConcordanceCounts.java @@ -3,7 +3,6 @@ import java.util.Arrays; import java.util.Collections; import java.util.EnumMap; -import java.util.HashMap; import java.util.HashSet; import java.util.List; import java.util.Map; diff --git a/src/main/java/picard/vcf/VcfFormatConverter.java b/src/main/java/picard/vcf/VcfFormatConverter.java index 39a94df18..da95c8dff 100644 --- a/src/main/java/picard/vcf/VcfFormatConverter.java +++ b/src/main/java/picard/vcf/VcfFormatConverter.java @@ -42,7 +42,6 @@ import picard.cmdline.CommandLineProgramProperties; import picard.cmdline.Option; import picard.cmdline.StandardOptionDefinitions; -import picard.cmdline.programgroups.SamOrBam; import picard.cmdline.programgroups.VcfOrBcf; import java.io.File; diff --git a/src/main/java/picard/vcf/filter/AlleleBalanceFilter.java b/src/main/java/picard/vcf/filter/AlleleBalanceFilter.java index 340d3d83c..f3e809fe7 100644 --- a/src/main/java/picard/vcf/filter/AlleleBalanceFilter.java +++ b/src/main/java/picard/vcf/filter/AlleleBalanceFilter.java @@ -26,9 +26,7 @@ import htsjdk.samtools.util.CollectionUtil; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Genotype; -import htsjdk.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.VariantContext; -import htsjdk.variant.variantcontext.VariantContextUtils; import htsjdk.variant.vcf.VCFFilterHeaderLine; import java.util.HashMap; diff --git a/src/main/java/picard/vcf/filter/DepthFilter.java b/src/main/java/picard/vcf/filter/DepthFilter.java index 4b3c07dc8..3a24acf03 100644 --- a/src/main/java/picard/vcf/filter/DepthFilter.java +++ b/src/main/java/picard/vcf/filter/DepthFilter.java @@ -24,12 +24,8 @@ package picard.vcf.filter; import htsjdk.variant.variantcontext.Genotype; -import htsjdk.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.VariantContext; -import java.util.HashMap; -import java.util.Map; - /** * Filters out a record if all variant samples have depth lower than the given value. */ diff --git a/src/main/java/picard/vcf/filter/GenotypeFilter.java b/src/main/java/picard/vcf/filter/GenotypeFilter.java index 03d3f0c21..063a1dd11 100644 --- a/src/main/java/picard/vcf/filter/GenotypeFilter.java +++ b/src/main/java/picard/vcf/filter/GenotypeFilter.java @@ -26,8 +26,6 @@ import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.VariantContext; -import java.util.Map; - /** * An interface for classes that perform Genotype filtration. Implementations are expected to take in a VariantContext * and a single Genotype and return either null (for no filter) or a specific filter string. diff --git a/src/main/java/picard/vcf/processor/util/PredicateFilterDecoratingClosableIterator.java b/src/main/java/picard/vcf/processor/util/PredicateFilterDecoratingClosableIterator.java index 7a8e6fbb2..f79afc7b0 100644 --- a/src/main/java/picard/vcf/processor/util/PredicateFilterDecoratingClosableIterator.java +++ b/src/main/java/picard/vcf/processor/util/PredicateFilterDecoratingClosableIterator.java @@ -27,7 +27,6 @@ import com.google.common.base.Preconditions; import com.google.common.base.Predicate; import com.google.common.collect.Iterators; -import htsjdk.samtools.util.Log; import htsjdk.samtools.util.CloseableIterator; import htsjdk.variant.variantcontext.VariantContext; diff --git a/src/test/java/picard/analysis/CollectInsertSizeMetricsTest.java b/src/test/java/picard/analysis/CollectInsertSizeMetricsTest.java index 6c7c9723e..3d6ebd865 100755 --- a/src/test/java/picard/analysis/CollectInsertSizeMetricsTest.java +++ b/src/test/java/picard/analysis/CollectInsertSizeMetricsTest.java @@ -26,7 +26,6 @@ import htsjdk.samtools.metrics.MetricsFile; import org.testng.Assert; import org.testng.annotations.Test; -import picard.PicardException; import picard.cmdline.CommandLineProgramTest; import picard.util.RExecutor; diff --git a/src/test/java/picard/analysis/CollectWgsMetricsFromSampledSitesTest.java b/src/test/java/picard/analysis/CollectWgsMetricsFromSampledSitesTest.java index 6f98fd891..bbf3df9e1 100644 --- a/src/test/java/picard/analysis/CollectWgsMetricsFromSampledSitesTest.java +++ b/src/test/java/picard/analysis/CollectWgsMetricsFromSampledSitesTest.java @@ -27,14 +27,11 @@ import org.testng.Assert; import org.testng.annotations.Test; import picard.cmdline.CommandLineProgramTest; -import picard.cmdline.PicardCommandLine; import java.io.File; import java.io.FileReader; import java.io.IOException; -import java.util.ArrayList; import java.util.HashMap; -import java.util.List; import java.util.Map; /** diff --git a/src/test/java/picard/analysis/CollectWgsMetricsTestUtils.java b/src/test/java/picard/analysis/CollectWgsMetricsTestUtils.java index 9364b559f..468a3853f 100644 --- a/src/test/java/picard/analysis/CollectWgsMetricsTestUtils.java +++ b/src/test/java/picard/analysis/CollectWgsMetricsTestUtils.java @@ -29,7 +29,6 @@ import htsjdk.variant.utils.SAMSequenceDictionaryExtractor; import java.io.File; -import java.io.IOError; import java.io.IOException; import java.util.stream.IntStream; diff --git a/src/test/java/picard/analysis/CollectWgsMetricsWithNonZeroCoverageTest.java b/src/test/java/picard/analysis/CollectWgsMetricsWithNonZeroCoverageTest.java index 4e9c1f0a8..e267a5407 100644 --- a/src/test/java/picard/analysis/CollectWgsMetricsWithNonZeroCoverageTest.java +++ b/src/test/java/picard/analysis/CollectWgsMetricsWithNonZeroCoverageTest.java @@ -4,7 +4,6 @@ import htsjdk.samtools.*; import htsjdk.samtools.util.Histogram; import htsjdk.samtools.metrics.MetricsFile; -import htsjdk.variant.utils.SAMSequenceDictionaryExtractor; import org.testng.Assert; import org.testng.annotations.Test; import picard.cmdline.CommandLineProgramTest; diff --git a/src/test/java/picard/cmdline/PicardCommandLineTest.java b/src/test/java/picard/cmdline/PicardCommandLineTest.java index f62d7501d..abad15f7d 100644 --- a/src/test/java/picard/cmdline/PicardCommandLineTest.java +++ b/src/test/java/picard/cmdline/PicardCommandLineTest.java @@ -2,8 +2,6 @@ import org.testng.annotations.Test; -import java.util.Collections; - /** * Created by farjoun on 9/10/15. */ diff --git a/src/test/java/picard/fingerprint/FingerprintCheckerTest.java b/src/test/java/picard/fingerprint/FingerprintCheckerTest.java index e54539f0e..e1eddca17 100644 --- a/src/test/java/picard/fingerprint/FingerprintCheckerTest.java +++ b/src/test/java/picard/fingerprint/FingerprintCheckerTest.java @@ -4,7 +4,6 @@ import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; -import picard.vcf.VcfTestUtils; import java.io.File; import java.io.IOException; diff --git a/src/test/java/picard/illumina/IlluminaLaneMetricsCollectorTest.java b/src/test/java/picard/illumina/IlluminaLaneMetricsCollectorTest.java index 4cb9880f5..3910852f4 100644 --- a/src/test/java/picard/illumina/IlluminaLaneMetricsCollectorTest.java +++ b/src/test/java/picard/illumina/IlluminaLaneMetricsCollectorTest.java @@ -1,9 +1,7 @@ package picard.illumina; -import htsjdk.samtools.SAMException; import htsjdk.samtools.util.IOUtil; import picard.illumina.parser.ReadStructure; -import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/picard/sam/MergeBamAlignmentTest.java b/src/test/java/picard/sam/MergeBamAlignmentTest.java index 968cc94ec..e88cd849a 100644 --- a/src/test/java/picard/sam/MergeBamAlignmentTest.java +++ b/src/test/java/picard/sam/MergeBamAlignmentTest.java @@ -563,7 +563,7 @@ public void testPairedMultiHitWithFiltering(final String description, final List final HitSpec secondHitSpec = secondOfPair.isEmpty()? null: secondOfPair.get(i); final SAMRecord first = makeRead(alignedHeader, firstUnmappedRec, firstHitSpec, true, i); final SAMRecord second = makeRead(alignedHeader, secondUnmappedRec, secondHitSpec, false, i); - if (first != null && second != null) SamPairUtil.setMateInfo(first, second, alignedHeader); + if (first != null && second != null) SamPairUtil.setMateInfo(first, second); if (first != null) { if (second == null) first.setMateUnmappedFlag(true); alignedWriter.addAlignment(first); @@ -938,7 +938,7 @@ public void testEarliestFragmentStrategyPaired() throws Exception { secondOfPair.setReadUnmappedFlag(true); secondOfPair.setReadPairedFlag(true); secondOfPair.setSecondOfPairFlag(true); - SamPairUtil.setMateInfo(firstOfPair, secondOfPair, header); + SamPairUtil.setMateInfo(firstOfPair, secondOfPair); final SAMFileWriter unmappedWriter = factory.makeSAMWriter(header, false, unmappedSam); unmappedWriter.addAlignment(firstOfPair); @@ -978,7 +978,7 @@ public void testEarliestFragmentStrategyPaired() throws Exception { secondOfPairAligned.setSecondOfPairFlag(true); secondOfPairAligned.setAttribute(SAMTag.HI.name(), i); - SamPairUtil.setMateInfo(firstOfPairAligned, secondOfPairAligned, header); + SamPairUtil.setMateInfo(firstOfPairAligned, secondOfPairAligned); alignedWriter.addAlignment(firstOfPairAligned); alignedWriter.addAlignment(secondOfPairAligned); diff --git a/src/test/java/picard/sam/RevertSamTest.java b/src/test/java/picard/sam/RevertSamTest.java index 95e0411df..5cb21477f 100755 --- a/src/test/java/picard/sam/RevertSamTest.java +++ b/src/test/java/picard/sam/RevertSamTest.java @@ -40,7 +40,6 @@ import java.io.File; import java.io.PrintWriter; import java.nio.file.Files; -import java.nio.file.Path; import java.nio.file.Paths; import java.util.ArrayList; import java.util.Arrays; diff --git a/src/test/java/picard/sam/testers/CleanSamTester.java b/src/test/java/picard/sam/testers/CleanSamTester.java index 4b9e6376e..5522e1b0e 100644 --- a/src/test/java/picard/sam/testers/CleanSamTester.java +++ b/src/test/java/picard/sam/testers/CleanSamTester.java @@ -11,7 +11,6 @@ import htsjdk.samtools.util.CloserUtil; import htsjdk.samtools.util.TestUtil; import org.testng.Assert; -import picard.cmdline.CommandLineProgram; import picard.sam.CleanSam; import java.io.PrintWriter; diff --git a/src/test/java/picard/util/BedToIntervalListTest.java b/src/test/java/picard/util/BedToIntervalListTest.java index 191bc4b6a..567b222de 100644 --- a/src/test/java/picard/util/BedToIntervalListTest.java +++ b/src/test/java/picard/util/BedToIntervalListTest.java @@ -2,14 +2,12 @@ import htsjdk.samtools.SAMException; import htsjdk.samtools.util.IOUtil; -import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import picard.PicardException; import java.io.File; import java.io.IOException; -import java.io.InputStream; /** * @author nhomer diff --git a/src/test/java/picard/util/IntervalListScattererTest.java b/src/test/java/picard/util/IntervalListScattererTest.java index ae106b8ca..960a5b8f9 100644 --- a/src/test/java/picard/util/IntervalListScattererTest.java +++ b/src/test/java/picard/util/IntervalListScattererTest.java @@ -194,7 +194,7 @@ private static IntervalList composeIntervalList(final IntervalList source, final private static Interval lookupIntervalContainingLocus(final IntervalList source, final String chromosome, final int startIndex) { for (final Interval interval : source) { - if (interval.getSequence().equals(chromosome) && startIndex >= interval.getStart() && startIndex <= interval.getEnd()) { + if (interval.getContig().equals(chromosome) && startIndex >= interval.getStart() && startIndex <= interval.getEnd()) { return interval; } } diff --git a/src/test/java/picard/vcf/CallingMetricAccumulatorTest.java b/src/test/java/picard/vcf/CallingMetricAccumulatorTest.java index 226eabc98..8e2d3dda3 100644 --- a/src/test/java/picard/vcf/CallingMetricAccumulatorTest.java +++ b/src/test/java/picard/vcf/CallingMetricAccumulatorTest.java @@ -2,10 +2,8 @@ import htsjdk.samtools.util.CollectionUtil; import htsjdk.variant.variantcontext.Allele; -import htsjdk.variant.variantcontext.FastGenotype; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.GenotypeBuilder; -import htsjdk.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextBuilder; import org.testng.Assert; @@ -15,9 +13,6 @@ import java.util.ArrayList; import java.util.Collections; import java.util.List; -import java.util.Map; - -import static org.testng.Assert.*; /** * Created by farjoun on 12/26/15. diff --git a/src/test/java/picard/vcf/GenotypeConcordanceTest.java b/src/test/java/picard/vcf/GenotypeConcordanceTest.java index 9913443aa..34214e2f5 100644 --- a/src/test/java/picard/vcf/GenotypeConcordanceTest.java +++ b/src/test/java/picard/vcf/GenotypeConcordanceTest.java @@ -27,7 +27,6 @@ import htsjdk.samtools.metrics.MetricsFile; import htsjdk.samtools.util.BufferedLineReader; import htsjdk.samtools.util.IOUtil; -import htsjdk.samtools.util.LineReader; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.GenotypeBuilder; @@ -46,12 +45,8 @@ import java.nio.file.Files; import java.nio.file.Path; import java.nio.file.Paths; -import java.nio.file.StandardCopyOption; import java.util.*; -import java.util.stream.Collectors; -import java.util.stream.Stream; import java.util.zip.GZIPInputStream; -import java.util.zip.GZIPOutputStream; public class GenotypeConcordanceTest {