Searched refs:isSecondOfPair (Results 1 – 13 of 13) sorted by relevance
57 return read.isSecondOfPair() ? PAIRED_INTERIOR : PAIRED_FIRST; in forRead()59 return read.isSecondOfPair() ? PAIRED_SECOND : PAIRED_UNKNOWN; in forRead()
29 else if (read1.isFirstOfPair() && read2.isSecondOfPair()) return -1; in compare()30 else if (read1.isSecondOfPair() && read2.isFirstOfPair()) return 1; in compare()
662 boolean isSecondOfPair();
543 public boolean isSecondOfPair() { in isSecondOfPair() method in SAMRecordToGATKReadAdapter
481 if ( read.isSecondOfPair() ) { in getSAMFlagsForRead()
67 final boolean isSecondInPair = read.isPaired() && read.isSecondOfPair(); in cycleKey()
133 if ( read.isSecondOfPair() ) { in add()
162 if (rec.isPaired() && rec.isSecondOfPair()) { in addRead()
100 if (read.isPaired() && read.isSecondOfPair()) { in addRead()
738 …Assert.assertEquals(read.isSecondOfPair(), expectedIsSecondOfPair, "Read second of pair setting in… in testReadNumber()742 …Assert.assertFalse(read.isSecondOfPair(), "Read should not be marked second of pair after setIsFir… in testReadNumber()746 …Assert.assertTrue(read.isSecondOfPair(), "Read should be marked second of pair after setIsSecondOf… in testReadNumber()770 …Assert.assertFalse(unpairedRead.isSecondOfPair(), "Unpaired read should not be marked as second of… in testGetReadNumberOfUnpairedRead()
231 return read.isSecondOfPair();}} in test()
92 } else if (read.isSecondOfPair()) { in clearReadAlignment()
395 if (rec.isSecondOfPair()) { in sanitize()