@Test(dataProvider = "HasWellDefinedFragmentSizeData") public void testHasWellDefinedFragmentSize(final String name, final GATKSAMRecord read, final boolean expected) { Assert.assertEquals(ReadUtils.hasWellDefinedFragmentSize(read), expected); }
if ( ! hasWellDefinedFragmentSize(read) ) { return CANNOT_COMPUTE_ADAPTOR_BOUNDARY; } else if ( read.getReadNegativeStrandFlag() ) {
clippedRead= ReadClipper.hardClipLowQualEnds( myRead, MIN_TAIL_QUALITY ); if ( dontUseSoftClippedBases || ! ReadUtils.hasWellDefinedFragmentSize(clippedRead) ) {
clippedRead= ReadClipper.hardClipLowQualEnds( myRead, MIN_TAIL_QUALITY ); if ( dontUseSoftClippedBases || ! ReadUtils.hasWellDefinedFragmentSize(clippedRead) ) {