} else { final String name = r.readName; final Map<String, CramCompressionRecord> mateMap = r.isSecondaryAlignment() ? secondaryMateMap : primaryMateMap; final CramCompressionRecord mate = mateMap.get(name); if (mate == null) {
} else { final String name = r.readName; final Map<String, CramCompressionRecord> mateMap = r.isSecondaryAlignment() ? secondaryMateMap : primaryMateMap; final CramCompressionRecord mate = mateMap.get(name); if (mate == null) {
} else { String name = r.readName; Map<String, CramCompressionRecord> mateMap = r.isSecondaryAlignment() ? secondaryMateMap : primaryMateMap; CramCompressionRecord mate = mateMap.get(name);
private static void copyFlags(final CramCompressionRecord cramRecord, final SAMRecord samRecord) { samRecord.setReadPairedFlag(cramRecord.isMultiFragment()); samRecord.setProperPairFlag(cramRecord.isProperPair()); samRecord.setReadUnmappedFlag(cramRecord.isSegmentUnmapped()); samRecord.setReadNegativeStrandFlag(cramRecord.isNegativeStrand()); samRecord.setFirstOfPairFlag(cramRecord.isFirstSegment()); samRecord.setSecondOfPairFlag(cramRecord.isLastSegment()); samRecord.setSecondaryAlignment(cramRecord.isSecondaryAlignment()); samRecord.setReadFailsVendorQualityCheckFlag(cramRecord.isVendorFiltered()); samRecord.setDuplicateReadFlag(cramRecord.isDuplicate()); samRecord.setSupplementaryAlignmentFlag(cramRecord.isSupplementary()); }
private static void copyFlags(final CramCompressionRecord cramRecord, final SAMRecord samRecord) { samRecord.setReadPairedFlag(cramRecord.isMultiFragment()); samRecord.setProperPairFlag(cramRecord.isProperPair()); samRecord.setReadUnmappedFlag(cramRecord.isSegmentUnmapped()); samRecord.setReadNegativeStrandFlag(cramRecord.isNegativeStrand()); samRecord.setFirstOfPairFlag(cramRecord.isFirstSegment()); samRecord.setSecondOfPairFlag(cramRecord.isLastSegment()); samRecord.setSecondaryAlignment(cramRecord.isSecondaryAlignment()); samRecord.setReadFailsVendorQualityCheckFlag(cramRecord.isVendorFiltered()); samRecord.setDuplicateReadFlag(cramRecord.isDuplicate()); samRecord.setSupplementaryAlignmentFlag(cramRecord.isSupplementary()); }