| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/clipping/ |
| H A D | ReadClipperUnitTest.java | 27 import static org.broadinstitute.hellbender.utils.read.ReadUtils.getSoftStart;
62 final int start = getSoftStart(read); in testHardClipByReferenceCoordinates()
89 …if (getSoftStart(read) == alnStart) { … in testHardClipByReferenceCoordinatesLeftTail()
242 Assert.assertEquals(getSoftStart(read), softStart); in testRevertSoftClippedBasesBeforeStartOfContig()
250 Assert.assertEquals(getSoftStart(reverted), expectedAlignmentStart); in testRevertSoftClippedBasesBeforeStartOfContig()
379 Assert.assertEquals(clippedRead.getStart(), getSoftStart(read)); in testRevertEntirelySoftClippedReads()
423 final int start = getSoftStart(read); in testSoftClipByReferenceCoordinates()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/fragments/ |
| H A D | FragmentUtils.java | 32 final boolean inOrder = pair.getLeft().getSoftStart() < pair.getRight().getSoftStart(); in adjustQualsOfOverlappingPairedFragments()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/ |
| H A D | GATKRead.java | 137 default int getSoftStart() { in getSoftStart() method
138 return ReadUtils.getSoftStart(this); in getSoftStart()
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| H A D | ReadUtils.java | 623 public static int getSoftStart(final GATKRead read) { in getSoftStart() method in ReadUtils
713 return getReadIndexForReferenceCoordinate(read.getSoftStart(), read.getCigar(), refCoord); in getReadIndexForReferenceCoordinate()
729 …Operator> offsetAndOperator = getReadIndexForReferenceCoordinate(read.getSoftStart(), read.getCiga… in getReadBaseQualityAtReferenceCoordinate()
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| H A D | SAMRecordToGATKReadAdapter.java | 153 public int getSoftStart() { in getSoftStart() method in SAMRecordToGATKReadAdapter
155 cachedSoftStart = ReadUtils.getSoftStart(this); in getSoftStart()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/ |
| H A D | AS_ReadPosRankSumTest.java | 83 …return super.isUsableRead(read, vc) && read.getSoftStart() <= vc.getEnd() + 1 && read.getSoftEnd()… in isUsableRead()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ |
| H A D | ReadPosRankSumTest.java | 50 …return super.isUsableRead(read, vc) && read.getSoftStart() <= vc.getEnd() + 1 && read.getSoftEnd()… in isUsableRead()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/clipping/ |
| H A D | ClippingOp.java | 133 final int newStart = read.getSoftStart(); in applyRevertSoftClippedBases()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ |
| H A D | HaplotypeCallerGenotypingEngine.java | 295 && read.getSoftStart() <= target.getEnd() in softUnclippedReadOverlapsInterval()
297 …&& read.getSoftStart() <= read.getSoftEnd(); // is this possible, ever? this test was performed be… in softUnclippedReadOverlapsInterval()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/ |
| H A D | DRAGENGenotypesModel.java | 246 …return (underlyingRead.getSoftStart() - underlyingRead.getUnclippedStart()) + offsetIntoReadForBas… in getForwardsFeatherEnd()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/ |
| H A D | OverhangFixingManager.java | 403 int softStart = read.getSoftStart(); in setRead()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/read/ |
| H A D | GATKReadAdaptersUnitTest.java | 267 Assert.assertEquals(read.getSoftStart(), 5); in testGetSoftStartAndEnd()
273 Assert.assertEquals(read.getSoftStart(), 4); in testGetSoftStartAndEnd()
279 Assert.assertEquals(read.getSoftStart(), 5); in testGetSoftStartAndEnd()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/recalibration/ |
| H A D | BaseRecalibrationEngine.java | 335 final int softStart = read.getSoftStart();
|