private void collectReadData(final SAMRecord record, final ReferenceSequence ref) {
metrics.TOTAL_READS++;
readLengthHistogram.increment(record.getReadBases().length);
if (!record.getReadFailsVendorQualityCheckFlag()) {
metrics.PF_READS++;
if (isNoiseRead(record)) metrics.PF_NOISE_READS++;
if (record.getReadUnmappedFlag()) {
// If the read is unmapped see if it's adapter sequence
final byte[] readBases = record.getReadBases();
if (!(record instanceof BAMRecord)) StringUtil.toUpperCase(readBases);
if (isAdapterSequence(readBases)) {
this.adapterReads++;
}
} else if (doRefMetrics) {
metrics.PF_READS_ALIGNED++;
if (!record.getReadNegativeStrandFlag()) numPositiveStrand++;
if (record.getReadPairedFlag() && !record.getMateUnmappedFlag()) {
metrics.READS_ALIGNED_IN_PAIRS++;
// Check that both ends have mapq > minimum
final Integer mateMq = record.getIntegerAttribute("MQ");
if (mateMq == null
|| mateMq >= MAPPING_QUALITY_THRESOLD
&& record.getMappingQuality() >= MAPPING_QUALITY_THRESOLD) {
++this.chimerasDenominator;
// With both reads mapped we can see if this pair is chimeric
if (Math.abs(record.getInferredInsertSize()) > maxInsertSize
|| !record.getReferenceIndex().equals(record.getMateReferenceIndex())) {
++this.chimeras;
}
}
}
}
}
}
static VariantContext reallyMergeIntoMNP(
VariantContext vc1, VariantContext vc2, ReferenceSequenceFile referenceFile) {
int startInter = vc1.getEnd() + 1;
int endInter = vc2.getStart() - 1;
byte[] intermediateBases = null;
if (startInter <= endInter) {
intermediateBases =
referenceFile.getSubsequenceAt(vc1.getChr(), startInter, endInter).getBases();
StringUtil.toUpperCase(intermediateBases);
}
MergedAllelesData mergeData =
new MergedAllelesData(
intermediateBases, vc1, vc2); // ensures that the reference allele is added
GenotypesContext mergedGenotypes = GenotypesContext.create();
for (final Genotype gt1 : vc1.getGenotypes()) {
Genotype gt2 = vc2.getGenotype(gt1.getSampleName());
List<Allele> site1Alleles = gt1.getAlleles();
List<Allele> site2Alleles = gt2.getAlleles();
List<Allele> mergedAllelesForSample = new LinkedList<Allele>();
/* NOTE: Since merged alleles are added to mergedAllelesForSample in the SAME order as in the input VC records,
we preserve phase information (if any) relative to whatever precedes vc1:
*/
Iterator<Allele> all2It = site2Alleles.iterator();
for (Allele all1 : site1Alleles) {
Allele all2 = all2It.next(); // this is OK, since allSamplesAreMergeable()
Allele mergedAllele = mergeData.ensureMergedAllele(all1, all2);
mergedAllelesForSample.add(mergedAllele);
}
double mergedGQ = Math.max(gt1.getLog10PError(), gt2.getLog10PError());
Set<String> mergedGtFilters =
new HashSet<
String>(); // Since gt1 and gt2 were unfiltered, the Genotype remains unfiltered
Map<String, Object> mergedGtAttribs = new HashMap<String, Object>();
PhaseAndQuality phaseQual = calcPhaseForMergedGenotypes(gt1, gt2);
if (phaseQual.PQ != null) mergedGtAttribs.put(ReadBackedPhasingWalker.PQ_KEY, phaseQual.PQ);
Genotype mergedGt =
new Genotype(
gt1.getSampleName(),
mergedAllelesForSample,
mergedGQ,
mergedGtFilters,
mergedGtAttribs,
phaseQual.isPhased);
mergedGenotypes.add(mergedGt);
}
String mergedName = mergeVariantContextNames(vc1.getSource(), vc2.getSource());
double mergedLog10PError = Math.min(vc1.getLog10PError(), vc2.getLog10PError());
Set<String> mergedFilters =
new HashSet<
String>(); // Since vc1 and vc2 were unfiltered, the merged record remains unfiltered
Map<String, Object> mergedAttribs = mergeVariantContextAttributes(vc1, vc2);
// ids
List<String> mergedIDs = new ArrayList<String>();
if (vc1.hasID()) mergedIDs.add(vc1.getID());
if (vc2.hasID()) mergedIDs.add(vc2.getID());
String mergedID =
mergedIDs.isEmpty()
? VCFConstants.EMPTY_ID_FIELD
: Utils.join(VCFConstants.ID_FIELD_SEPARATOR, mergedIDs);
VariantContextBuilder mergedBuilder =
new VariantContextBuilder(
mergedName,
vc1.getChr(),
vc1.getStart(),
vc2.getEnd(),
mergeData.getAllMergedAlleles())
.id(mergedID)
.genotypes(mergedGenotypes)
.log10PError(mergedLog10PError)
.filters(mergedFilters)
.attributes(mergedAttribs);
VariantContextUtils.calculateChromosomeCounts(mergedBuilder, true);
return mergedBuilder.make();
}