Searched refs:getSoftEnd (Results 1 – 11 of 11) sorted by relevance
148 default int getSoftEnd() { in getSoftEnd() method149 return ReadUtils.getSoftEnd(this); in getSoftEnd()
162 public int getSoftEnd() { in getSoftEnd() method in SAMRecordToGATKReadAdapter164 cachedSoftEnd = ReadUtils.getSoftEnd(this); in getSoftEnd()
646 public static int getSoftEnd(final GATKRead read) { in getSoftEnd() method in ReadUtils
26 import static org.broadinstitute.hellbender.utils.read.ReadUtils.getSoftEnd;63 final int stop = getSoftEnd(read); in testHardClipByReferenceCoordinates()109 …if (getSoftEnd(read) == alnEnd) { … in testHardClipByReferenceCoordinatesRightTail()424 final int stop = getSoftEnd(read); in testSoftClipByReferenceCoordinates()
83 …UsableRead(read, vc) && read.getSoftStart() <= vc.getEnd() + 1 && read.getSoftEnd() >= vc.getStart… in isUsableRead()
50 …UsableRead(read, vc) && read.getSoftStart() <= vc.getEnd() + 1 && read.getSoftEnd() >= vc.getStart… in isUsableRead()
296 && read.getSoftEnd() >= target.getStart() in softUnclippedReadOverlapsInterval()297 …&& read.getSoftStart() <= read.getSoftEnd(); // is this possible, ever? this test was performed be… in softUnclippedReadOverlapsInterval()
250 …return (underlyingRead.getUnclippedEnd() - underlyingRead.getSoftEnd()) + (underlyingRead.getLengt… in getReverseFeatherEnd()
404 int softEnd = read.getSoftEnd(); in setRead()
268 Assert.assertEquals(read.getSoftEnd(), 7); in testGetSoftStartAndEnd()274 Assert.assertEquals(read.getSoftEnd(), 7); in testGetSoftStartAndEnd()280 Assert.assertEquals(read.getSoftEnd(), 8); in testGetSoftStartAndEnd()
336 final int softEnd = read.getSoftEnd();