@Override public int getLocalMapq() { return local.getMappingQuality(); } @Override
public boolean filterOut(SAMRecord rec) { return (rec.getMappingQuality() == QualityUtils.MAPPING_QUALITY_UNAVAILABLE); } }
public boolean filterOut(SAMRecord rec) { return (rec.getMappingQuality() == 0); } }
public boolean filterOut(SAMRecord rec) { return (rec.getMappingQuality() < MIN_MAPPING_QUALTY_SCORE); } }
public boolean filterOut(SAMRecord rec) { return (rec.getMappingQuality() < MIN_MAPPING_QUALTY_SCORE); } }
@Override public boolean filterOut(final SAMRecord record) { return record.getMappingQuality() < this.minimumMappingQuality; }
@Override public boolean reallyFilterOut(final SAMRecord record) { return record.getMappingQuality() < minMapq; } }
@Override public AlignmentFilters<SAMRecord> addMappingQualityFilter(int mappingQuality) { filters.add(samRecord -> samRecord.getMappingQuality() >= mappingQuality); return this; }
public boolean filterOut(SAMRecord rec) { if (rec.getMappingQuality() == reassignMappingQualityFrom) rec.setMappingQuality(reassignMappingQualityTo); return false; } }
private boolean isHighQualityMapping(final SAMRecord record) { return !record.getReadFailsVendorQualityCheckFlag() && record.getMappingQuality() >= MAPPING_QUALITY_THRESHOLD; }
@Override public int getRemoteMapq() { return getNonReferenceRead().getMappingQuality(); } @Override
private boolean isHighQualityMapping(final SAMRecord record) { return !record.getReadFailsVendorQualityCheckFlag() && record.getMappingQuality() >= MAPPING_QUALITY_THRESHOLD; }
@Override public int getMappingQuality() { if (!initializedFields.contains(LazyField.MAPPING_QUALITY)) { setMappingQuality(getMappingQualityImpl()); } return super.getMappingQuality(); }
public void considerBest(final SAMRecord firstEnd, final SAMRecord secondEnd) { final int thisPairMapq = SAMUtils.combineMapqs(firstEnd.getMappingQuality(), secondEnd.getMappingQuality()); final int thisDistance = CoordMath.getLength(Math.min(firstEnd.getAlignmentStart(), secondEnd.getAlignmentStart()), Math.max(firstEnd.getAlignmentEnd(), secondEnd.getAlignmentEnd())); if (thisDistance > bestDistance || (thisDistance == bestDistance && thisPairMapq > bestPairMapq)) { bestDistance = thisDistance; bestPairMapq = thisPairMapq; bestAlignmentPairs.clear(); bestAlignmentPairs.add(new AbstractMap.SimpleEntry<SAMRecord, SAMRecord>(firstEnd, secondEnd)); } else if (thisDistance == bestDistance && thisPairMapq == bestPairMapq) { bestAlignmentPairs.add(new AbstractMap.SimpleEntry<SAMRecord, SAMRecord>(firstEnd, secondEnd)); } }
@Override public int getMappingQuality() { if (!initializedFields.contains(LazyField.MAPPING_QUALITY)) { setMappingQuality(getMappingQualityImpl()); } return super.getMappingQuality(); }
public boolean filterOut(SAMRecord rec) { final String ORIGINAL_CIGAR_TAG = "OC"; if (rec.getAttribute(ORIGINAL_CIGAR_TAG) != null) rec.setMappingQuality(rec.getMappingQuality() - 10); return false; } }
public int compare(final SAMRecord rec1, final SAMRecord rec2) { if (rec1.getReadUnmappedFlag()) { if (rec2.getReadUnmappedFlag()) return 0; else return 1; } else if (rec2.getReadUnmappedFlag()) { return -1; } return -SAMUtils.compareMapqs(rec1.getMappingQuality(), rec2.getMappingQuality()); } }
public int compare(final SAMRecord rec1, final SAMRecord rec2) { if (rec1.getReadUnmappedFlag()) { if (rec2.getReadUnmappedFlag()) return 0; else return 1; } else if (rec2.getReadUnmappedFlag()) { return -1; } return -SAMUtils.compareMapqs(rec1.getMappingQuality(), rec2.getMappingQuality()); } }
private boolean shouldAssemble(SAMRecord read) { return ( (!read.getDuplicateReadFlag()) && (!read.getReadFailsVendorQualityCheckFlag()) && read.getReadLength() > 0 && (read.getMappingQuality() >= this.minMapqForAssembly || read.getReadUnmappedFlag()) && SAMRecordUtils.isPrimary(read)); // Was previously an id check, so supplemental / secondary alignments could be included }
public static boolean meetsAnchorCriteria(SAMEvidenceSource source, SAMRecord read) { return read.getReadPairedFlag() && !read.getReadUnmappedFlag() && !read.getReadFailsVendorQualityCheckFlag() && read.getMappingQuality() >= source.getContext().getConfig().minMapq && !SAMRecordUtil.estimatedReadsOverlap(read, PairOrientation.FR, source.getMetrics().getIdsvMetrics().MAX_READ_LENGTH - source.getMetrics().getMaxSoftClipLength()) && !source.getReadPairConcordanceCalculator().isConcordant(read); } public static boolean meetsRemoteCriteria(SAMEvidenceSource source, SAMRecord read) {