/** * Determines whether a SAMRecord matches this filter * * @param record the SAMRecord to evaluate * @return true if the SAMRecord matches the filter, otherwise false */ @Override public boolean filterOut(final SAMRecord record) { return record.getReadFailsVendorQualityCheckFlag(); }
/** * Determines whether a SAMRecord matches this filter * * @param record the SAMRecord to evaluate * @return true if the SAMRecord matches the filter, otherwise false */ public boolean filterOut(final SAMRecord record) { return record.getReadFailsVendorQualityCheckFlag(); }
/** * Determines whether a SAMRecord matches this filter * * @param record the SAMRecord to evaluate * @return true if the SAMRecord matches the filter, otherwise false */ @Override public boolean filterOut(final SAMRecord record) { return record.getReadFailsVendorQualityCheckFlag(); }
public boolean filterOut( final SAMRecord read ) { return read.getReadFailsVendorQualityCheckFlag(); } }
/** * Determines whether a pair of SAMRecord matches this filter * * @param first the first SAMRecord to evaluate * @param second the second SAMRecord to evaluate * * @return true if the SAMRecords matches the filter, otherwise false */ @Override public boolean filterOut(final SAMRecord first, final SAMRecord second) { // if either fails, exclude them both return (first.getReadFailsVendorQualityCheckFlag() || second.getReadFailsVendorQualityCheckFlag()); } }
/** * Determines whether a pair of SAMRecord matches this filter * * @param first the first SAMRecord to evaluate * @param second the second SAMRecord to evaluate * * @return true if the SAMRecords matches the filter, otherwise false */ public boolean filterOut(final SAMRecord first, final SAMRecord second) { // if either fails, exclude them both return (first.getReadFailsVendorQualityCheckFlag() || second.getReadFailsVendorQualityCheckFlag()); } }
/** * Determines whether a pair of SAMRecord matches this filter * * @param first the first SAMRecord to evaluate * @param second the second SAMRecord to evaluate * * @return true if the SAMRecords matches the filter, otherwise false */ @Override public boolean filterOut(final SAMRecord first, final SAMRecord second) { // if either fails, exclude them both return (first.getReadFailsVendorQualityCheckFlag() || second.getReadFailsVendorQualityCheckFlag()); } }
private boolean isHighQualityMapping(final SAMRecord record) { return !record.getReadFailsVendorQualityCheckFlag() && record.getMappingQuality() >= MAPPING_QUALITY_THRESHOLD; }
private boolean isHighQualityMapping(final SAMRecord record) { return !record.getReadFailsVendorQualityCheckFlag() && record.getMappingQuality() >= MAPPING_QUALITY_THRESHOLD; }
/** * Returns true if we don't think this read is eligible for the BAQ calculation. Examples include non-PF reads, * duplicates, or unmapped reads. Used by baqRead to determine if a read should fall through the calculation. * * @param read * @return */ public boolean excludeReadFromBAQ(final SAMRecord read) { // keeping mapped reads, regardless of pairing status, or primary alignment status. return read.getReadUnmappedFlag() || read.getReadFailsVendorQualityCheckFlag() || read.getDuplicateReadFlag(); } }
@Override protected void acceptRead(final SAMRecord rec, final ReferenceSequence ref) { if ((PF_READS_ONLY) && (rec.getReadFailsVendorQualityCheckFlag())) { return; } if ((ALIGNED_READS_ONLY) && (rec.getReadUnmappedFlag())) { return; } if (rec.isSecondaryOrSupplementary()) { return; } hist.addRecord(rec); }
@Override protected void acceptRead(final SAMRecord rec, final ReferenceSequence ref) { if ((PF_READS_ONLY) && (rec.getReadFailsVendorQualityCheckFlag())) { return; } if ((ALIGNED_READS_ONLY) && (rec.getReadUnmappedFlag())) { return; } if (rec.isSecondaryOrSupplementary()) { return; } hist.addRecord(rec); }
public static final boolean excludeRead(SAMRecord read) { return read.getReadUnmappedFlag() || read.getReadFailsVendorQualityCheckFlag() || read.getDuplicateReadFlag() || read.getNotPrimaryAlignmentFlag(); }
@Override protected void acceptRead(final SAMRecord rec, final ReferenceSequence ref) { // Skip unwanted records if (PF_READS_ONLY && rec.getReadFailsVendorQualityCheckFlag()) return; if (ALIGNED_READS_ONLY && rec.getReadUnmappedFlag()) return; if (rec.isSecondaryOrSupplementary()) return; q.addRecord(rec); oq.addRecord(rec); }
@Override protected void acceptRead(final SAMRecord rec, final ReferenceSequence ref) { // Skip unwanted records if (PF_READS_ONLY && rec.getReadFailsVendorQualityCheckFlag()) return; if (ALIGNED_READS_ONLY && rec.getReadUnmappedFlag()) return; if (rec.isSecondaryOrSupplementary()) return; q.addRecord(rec); oq.addRecord(rec); }
public boolean filterOut(SAMRecord read) { return (! read.getReadPairedFlag() ) || read.getMateUnmappedFlag() || read.getDuplicateReadFlag() || read.getReadFailsVendorQualityCheckFlag() || (read.getMateNegativeStrandFlag() == read.getReadNegativeStrandFlag()); } }
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 meetsRemoteCriteria(SAMEvidenceSource source, SAMRecord read) { return read.getReadPairedFlag() && !read.getMateUnmappedFlag() // other side has to be an anchor && !read.getReadFailsVendorQualityCheckFlag() && (meetsDPRemoteCriteria(source, read) || meetsOEARemoteCriteria(source, read)) && !source.getContext().getConfig().adapters.containsAdapter(read); } private static boolean meetsDPRemoteCriteria(SAMEvidenceSource source, SAMRecord read) {
private static boolean meetsDPRemoteCriteria(SAMEvidenceSource source, SAMRecord read) { return read.getReadPairedFlag() && !read.getReadUnmappedFlag() && !read.getReadFailsVendorQualityCheckFlag() && !SAMRecordUtil.estimatedReadsOverlap(read, PairOrientation.FR, source.getMetrics().getIdsvMetrics().MAX_READ_LENGTH - source.getMetrics().getMaxSoftClipLength()) && !source.getReadPairConcordanceCalculator().isConcordant(read); } private static boolean meetsOEARemoteCriteria(SAMEvidenceSource source, SAMRecord read) {
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) {