/** * @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.getDuplicateReadFlag(); }
/** * @param record the SAMRecord to evaluate * @return true if the SAMRecord matches the filter, otherwise false */ public boolean filterOut(final SAMRecord record) { return record.getDuplicateReadFlag(); }
public boolean filterOut( final SAMRecord read ) { return read.getDuplicateReadFlag(); } }
/** * @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.getDuplicateReadFlag(); }
@Override public boolean reallyFilterOut(final SAMRecord record) { return record.getDuplicateReadFlag(); } }
@Override public boolean reallyFilterOut(final SAMRecord record) { return record.getDuplicateReadFlag(); } }
@Override public AlignmentFilters<SAMRecord> addDuplicatedFilter() { filters.add(samRecord -> !samRecord.getDuplicateReadFlag()); return this; }
@Override protected void acceptRead(final SAMRecord record, final ReferenceSequence ref) { if (record.getDuplicateReadFlag() && !INCLUDE_DUPLICATES) return; multiCollector.acceptRecord(record, ref); }
@Override protected void acceptRead(final SAMRecord record, final ReferenceSequence ref) { if (record.getDuplicateReadFlag() && !INCLUDE_DUPLICATES) return; multiCollector.acceptRecord(record, ref); }
@Override protected void acceptRead(final SAMRecord rec, final ReferenceSequence ref) { if (rec.getDuplicateReadFlag() && !INCLUDE_DUPLICATES) return; for (SAMTagAndValue attr : rec.getAttributes()) { String tag = attr.tag; TagSummaryMetrics metric = tags.get(tag); if (metric == null) { metric = new TagSummaryMetrics(); metric.TAG = tag; metric.COUNT = 0; tags.put(tag, metric); } metric.COUNT++; } }
/** * 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(); } }
public static final boolean excludeRead(SAMRecord read) { return read.getReadUnmappedFlag() || read.getReadFailsVendorQualityCheckFlag() || read.getDuplicateReadFlag() || read.getNotPrimaryAlignmentFlag(); }
public void addRecord(final SAMRecord record) { final String key = samRecordToDuplicatesFlagsKey(record); Assert.assertFalse(this.duplicateFlags.containsKey(key)); this.duplicateFlags.put(key, record.getDuplicateReadFlag()); this.samRecordSetBuilder.addRecord(record); }
public boolean[] shouldExtract(List<SAMRecord> records, ReferenceLookup lookup) { boolean hasConsistentReadPair = hasReadPairingConsistentWithReference(getReadPairConcordanceCalculator(), records); boolean[] hasConsistentReadAlignment = hasReadAlignmentConsistentWithReference(records); boolean[] extract = new boolean[records.size()]; for (int i = 0; i < records.size(); i++) { SAMRecord r = records.get(i); extract[i] = !hasConsistentReadAlignment[SAMRecordUtil.getSegmentIndex(r)] && !readfilter.filterOut(r); // supp records should use the primary alignment when considering concordance extract[i] |= !hasConsistentReadPair && !pairfilter.filterOut(primaryAlignmentForSupplementary(r)); extract[i] &= (!r.getDuplicateReadFlag() || INCLUDE_DUPLICATES); } return extract; } @Override
/** * Gets a SAMRecord if one is available after marking. This enforces that we return records in the original * coordinate sort order in a stable fashion. * * @return record representing the head of the alignment-start sorted buffer, or null if the head record has not yet been duplicate marked */ private SAMRecord flush() { // Check that there is at least one record in the coordinate-sorted buffer, and that the head record has been through duplicate-marking while (!outputBuffer.isEmpty() && outputBuffer.canEmit()) { // the buffer contains wrapped SAMRecords, which we want to unwrap final SAMRecord record = outputBuffer.next().getRecord(); // If this read is a duplicate, do we want to remove it (continue the loop) or return it for emission? if (!removeDuplicates || !record.getDuplicateReadFlag()) { return record; } } return null; }
public boolean filterOut(SAMRecord read) { return (! read.getReadPairedFlag() ) || read.getMateUnmappedFlag() || read.getDuplicateReadFlag() || read.getReadFailsVendorQualityCheckFlag() || (read.getMateNegativeStrandFlag() == read.getReadNegativeStrandFlag()); } }
@Override protected void acceptRead(SAMRecord record, ReferenceSequence refSeq) { if (record.getDuplicateReadFlag() && !INCLUDE_DUPLICATES) return; ReadGcSummary gc = new ReadGcSummary(record, refSeq, UNPAIRED_FRAGMENT_SIZE, getReadPairConcordanceCalculator()); if (ica_gc != null) { ica_gc.add(record, gc, gcAdjust.adjustmentMultiplier((int)gc.gcPercentage)); } ica_raw.add(record, gc, 1.0); } @Override
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 }
@Override public void acceptRecord(final SAMRecord record, final ReferenceSequence refSeq) { if (!record.getReadPairedFlag() || record.getReadUnmappedFlag() || record.getMateUnmappedFlag() || record.getFirstOfPairFlag() || record.isSecondaryOrSupplementary() || (record.getDuplicateReadFlag() && !this.includeDuplicates) || record.getInferredInsertSize() == 0) { return; } super.acceptRecord(record, refSeq); }
@Override public void acceptRecord(final SAMRecord record, final ReferenceSequence refSeq) { if (!record.getReadPairedFlag() || record.getReadUnmappedFlag() || record.getMateUnmappedFlag() || record.getFirstOfPairFlag() || record.isSecondaryOrSupplementary() || (record.getDuplicateReadFlag() && !this.includeDuplicates) || record.getInferredInsertSize() == 0) { return; } super.acceptRecord(record, refSeq); }