if (firstEnd.getAlignmentEnd() != right) firstEnd.templateSize = tlen; else if (firstEnd.isFirstSegment()) firstEnd.templateSize = tlen; else if (secondEnd.getAlignmentEnd() != right) secondEnd.templateSize = tlen; else if (secondEnd.isFirstSegment()) secondEnd.templateSize = tlen; else
@SuppressWarnings("SimplifiableIfStatement") @Override public boolean equals(final Object obj) { if (!(obj instanceof CramCompressionRecord)) return false; final CramCompressionRecord cramRecord = (CramCompressionRecord) obj; if (alignmentStart != cramRecord.alignmentStart) return false; if (isNegativeStrand() != cramRecord.isNegativeStrand()) return false; if (isVendorFiltered() != cramRecord.isVendorFiltered()) return false; if (isSegmentUnmapped() != cramRecord.isSegmentUnmapped()) return false; if (readLength != cramRecord.readLength) return false; if (isLastSegment() != cramRecord.isLastSegment()) return false; if (recordsToNextFragment != cramRecord.recordsToNextFragment) return false; if (isFirstSegment() != cramRecord.isFirstSegment()) return false; if (mappingQuality != cramRecord.mappingQuality) return false; if (!deepEquals(readFeatures, cramRecord.readFeatures)) return false; if (!Arrays.equals(readBases, cramRecord.readBases)) return false; return Arrays.equals(qualityScores, cramRecord.qualityScores) && areEqual(flags, cramRecord.flags) && areEqual(readName, cramRecord.readName); }
@SuppressWarnings("SimplifiableIfStatement") @Override public boolean equals(final Object obj) { if (!(obj instanceof CramCompressionRecord)) return false; final CramCompressionRecord cramRecord = (CramCompressionRecord) obj; if (alignmentStart != cramRecord.alignmentStart) return false; if (isNegativeStrand() != cramRecord.isNegativeStrand()) return false; if (isVendorFiltered() != cramRecord.isVendorFiltered()) return false; if (isSegmentUnmapped() != cramRecord.isSegmentUnmapped()) return false; if (readLength != cramRecord.readLength) return false; if (isLastSegment() != cramRecord.isLastSegment()) return false; if (recordsToNextFragment != cramRecord.recordsToNextFragment) return false; if (isFirstSegment() != cramRecord.isFirstSegment()) return false; if (mappingQuality != cramRecord.mappingQuality) return false; if (!deepEquals(readFeatures, cramRecord.readFeatures)) return false; if (!Arrays.equals(readBases, cramRecord.readBases)) return false; return Arrays.equals(qualityScores, cramRecord.qualityScores) && areEqual(flags, cramRecord.flags) && areEqual(readName, cramRecord.readName); }
last = last.next; if ((r.isFirstSegment() && last.isLastSegment()) || (last.isFirstSegment() && r.isLastSegment())) {
while (last.next != null) last = last.next; if (cramRecord.isFirstSegment() && last.isLastSegment()) {
while (last.next != null) last = last.next; if (cramRecord.isFirstSegment() && last.isLastSegment()) {
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()); }