if (!record.isMultiFragment() || record.isDetached()) { record.recordsToNextFragment = -1;
final Map<String, CramCompressionRecord> secondaryMateMap = new TreeMap<String, CramCompressionRecord>(); for (final CramCompressionRecord r : cramRecords) { if (!r.isMultiFragment()) { r.setDetached(true);
final Map<String, CramCompressionRecord> secondaryMateMap = new TreeMap<String, CramCompressionRecord>(); for (final CramCompressionRecord r : cramRecords) { if (!r.isMultiFragment()) { r.setDetached(true);
if (!record.isMultiFragment() || record.isDetached()) { record.recordsToNextFragment = -1;
if (!record.isMultiFragment() || record.isDetached()) { record.recordsToNextFragment = -1;
Map<String, CramCompressionRecord> secondaryMateMap = new TreeMap<String, CramCompressionRecord>(); for (CramCompressionRecord r : cramRecords) { if (!r.isMultiFragment()) { r.setDetached(true);
if (!record.isMultiFragment() || record.isDetached()) { record.recordsToNextFragment = -1;
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()); }