Searched refs:setIsProperlyPaired (Results 1 – 9 of 9) sorted by relevance
35 read1.setIsProperlyPaired(true); in testInGoodPair()42 read1.setIsProperlyPaired(false); in testInGoodPair()44 read1.setIsProperlyPaired(true); in testInGoodPair()124 splicedReadImproperlyPaired.setIsProperlyPaired(false); in testGetAlignmentIntervalsDataProvider()137 splicedReadImproperlyPairedReverseStrand.setIsProperlyPaired(false); in testGetAlignmentIntervalsDataProvider()178 unsplicedReadImproperlyPaired.setIsProperlyPaired(false); in testGetAlignmentIntervalsDataProvider()186 unsplicedReadImproperlyPairedReverseStrand.setIsProperlyPaired(false); in testGetAlignmentIntervalsDataProvider()195 read.setIsProperlyPaired(true); in pairRead()
57 read.setIsProperlyPaired(true); in makeRead()153 read.setIsProperlyPaired(false); in testGetAdaptorBoundary()161 read.setIsProperlyPaired(true); in testGetAdaptorBoundary()169 read.setIsProperlyPaired(true); in testGetAdaptorBoundary()276 read.setIsProperlyPaired(true); in makeHasWellDefinedFragmentSizeData()295 bad.setIsProperlyPaired(false); in makeHasWellDefinedFragmentSizeData()
564 read.setIsProperlyPaired(true); in testIsPaired()568 read.setIsProperlyPaired(false); in testIsPaired()573 read.setIsProperlyPaired(true); in testIsPaired()1076 read.setIsProperlyPaired(true); in testSAMStringIsPaired()1080 read.setIsProperlyPaired(false); in testSAMStringIsPaired()
549 void setIsProperlyPaired( final boolean isProperlyPaired );
483 left.setIsProperlyPaired(true); in createPair()484 right.setIsProperlyPaired(true); in createPair()
416 public void setIsProperlyPaired( final boolean isProperlyPaired ) { in setIsProperlyPaired() method in SAMRecordToGATKReadAdapter
855 read.setIsProperlyPaired(true); in testNotProperlyPaired()857 read.setIsProperlyPaired(false); in testNotProperlyPaired()899 read.setIsProperlyPaired(true); in testProperlyPairedReadFilter()
550 rec.setIsProperlyPaired(false);
727 read.setIsProperlyPaired(true); in makeAdapterClippingTest()