private static void setNextMate(final CramCompressionRecord record, final CramCompressionRecord next) { record.mateAlignmentStart = next.alignmentStart; record.setMateUnmapped(next.isSegmentUnmapped()); record.setMateNegativeStrand(next.isNegativeStrand()); record.mateSequenceID = next.sequenceId; if (record.mateSequenceID == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) record.mateAlignmentStart = SAMRecord.NO_ALIGNMENT_START; }
private static void setNextMate(CramCompressionRecord r, CramCompressionRecord next) { r.mateAlignmentStart = next.alignmentStart; r.setMateUnmapped(next.isSegmentUnmapped()); r.setMateNegativeStrand(next.isNegativeStrand()); r.mateSequenceID = next.sequenceId; if (r.mateSequenceID == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) r.mateAlignmentStart = SAMRecord.NO_ALIGNMENT_START; }
private static void setNextMate(final CramCompressionRecord record, final CramCompressionRecord next) { record.mateAlignmentStart = next.alignmentStart; record.setMateUnmapped(next.isSegmentUnmapped()); record.setMateNegativeStrand(next.isNegativeStrand()); record.mateSequenceID = next.sequenceId; if (record.mateSequenceID == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) record.mateAlignmentStart = SAMRecord.NO_ALIGNMENT_START; }
private static void setNextMate(final CramCompressionRecord record, final CramCompressionRecord next) { record.mateAlignmentStart = next.alignmentStart; record.setMateUnmapped(next.isSegmentUnmapped()); record.setMateNegativeStrand(next.isNegativeStrand()); record.mateSequenceID = next.sequenceId; if (record.mateSequenceID == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) record.mateAlignmentStart = SAMRecord.NO_ALIGNMENT_START; }
cramRecord.mateAlignmentStart = record.getMateAlignmentStart(); cramRecord.setMateUnmapped(record.getMateUnmappedFlag()); cramRecord.setMateNegativeStrand(record.getMateNegativeStrandFlag()); cramRecord.mateSequenceID = record.getMateReferenceIndex(); } else cramRecord.mateSequenceID = -1;
cramRecord.mateAlignmentStart = record.getMateAlignmentStart(); cramRecord.setMateUnmapped(record.getMateUnmappedFlag()); cramRecord.setMateNegativeStrand(record.getMateNegativeStrandFlag()); cramRecord.mateSequenceID = record.getMateReferenceIndex(); } else cramRecord.mateSequenceID = -1;