public VariantContextWriter reduce(final VariantContext vc, final VariantContextWriter writer) { if ( vc != null ) writer.add(vc); return writer; }
@Override public void add(final VariantContext vc) { for ( final VariantContextWriter writer : writers ) writer.add(vc); }
@Override public Integer reduce(final List<VariantContext> callsInRegion, final Integer numCalledRegions) { for( final VariantContext call : callsInRegion ) { vcfWriter.add( call ); } return (callsInRegion.isEmpty() ? 0 : 1) + numCalledRegions; }
@Override public Integer reduce(List<VariantContext> callsInRegion, Integer numCalledRegions) { for( final VariantContext call : callsInRegion ) { vcfWriter.add( call ); } return (callsInRegion.isEmpty() ? 0 : 1) + numCalledRegions; }
/** * Flush the current hom-ref block, if necessary, to the underlying writer, and reset the currentBlock to null */ private void emitCurrentBlock() { if ( currentBlock != null ) { // there's actually some work to do underlyingWriter.add(blockToVCF(currentBlock)); currentBlock = null; } }
/** * @{inheritDoc} */ public void add(VariantContext vc) { outputTracker.getStorage(this).add(vc); }
private void writeVCF(VariantContext vc) { if (samplesToPhase == null || vc.isNotFiltered()) //if ( samplesToPhase == null || (vc.isVariant() && vc.isNotFiltered())) // if we are only operating on specific samples, don't write out all sites, just those where the VC is variant writer.add(vc); }
public void onTraversalDone(Integer result) { logger.info("Outputting validation sites..."); ArrayList<VariantContext> selectedSites = frequencyModeSelector.selectValidationSites(numValidationSites); for (VariantContext vc : selectedSites) { vcfWriter.add(vc); } logger.info(result + " records processed."); }
@Override public boolean write(List<T> list) { List<VariantContext> contexts = converter.apply(list); for (VariantContext variantContext : contexts) { variantContextWriter.add(variantContext); } return true; }
private void writeOne(final VariantContext vc, final String set, final String status) { final Map<String, Object> attrs = new HashMap<>(); if ( SET_KEY != null && set != null ) attrs.put(SET_KEY, set); if ( STATUS_KEY != null && status != null ) attrs.put(STATUS_KEY, status); writer.add(new VariantContextBuilder(vc).attributes(attrs).make()); }
protected void writeVcf(File vcf, Iterable<VariantContext> calls) { VariantContextWriter writer = context.getVariantContextWriter(vcf, true); for (VariantContext vc : calls) { writer.add(vc); } writer.close(); } protected String getChr() { return chr; }
protected void writeRecord(VariantContext vc) { final GenotypesContext gc = vc.getGenotypes(); if (gc instanceof LazyParsingGenotypesContext) ((LazyParsingGenotypesContext)gc).getParser().setHeaderDataCache( gc instanceof LazyVCFGenotypesContext ? vcfHeaderDataCache : bcfHeaderDataCache); writer.add(vc); } }
protected void writeRecord(VariantContext vc) { final GenotypesContext gc = vc.getGenotypes(); if (gc instanceof LazyParsingGenotypesContext) ((LazyParsingGenotypesContext)gc).getParser().setHeaderDataCache( gc instanceof LazyVCFGenotypesContext ? vcfHeaderDataCache : bcfHeaderDataCache); writer.add(vc); } }
protected void writeRecord(VariantContext vc) { final GenotypesContext gc = vc.getGenotypes(); if (gc instanceof LazyParsingGenotypesContext) ((LazyParsingGenotypesContext)gc).getParser().setHeaderDataCache( gc instanceof LazyVCFGenotypesContext ? vcfHeaderDataCache : bcfHeaderDataCache); writer.add(vc); } }
protected void writeRecord(VariantContext vc) { final GenotypesContext gc = vc.getGenotypes(); if (gc instanceof LazyParsingGenotypesContext) ((LazyParsingGenotypesContext)gc).getParser().setHeaderDataCache( gc instanceof LazyVCFGenotypesContext ? vcfHeaderDataCache : bcfHeaderDataCache); writer.add(vc); } }
protected void writeRecord(VariantContext vc) { final GenotypesContext gc = vc.getGenotypes(); if (gc instanceof LazyParsingGenotypesContext) ((LazyParsingGenotypesContext)gc).getParser().setHeaderDataCache( gc instanceof LazyVCFGenotypesContext ? vcfHeaderDataCache : bcfHeaderDataCache); writer.add(vc); } }
private void rejectVariant(final VariantContext ctx, final String reason) { rejects.add(new VariantContextBuilder(ctx).filter(reason).make()); failedLiftover++; trackLiftedVariantContig(rejectsByContig, ctx.getContig()); }
private static void writeVCsToFile(final VariantContextWriter writer, final VCFHeader header, final Iterable<VariantContext> vcs) { // write writer.writeHeader(header); for ( VariantContext vc : vcs ) if (vc != null) writer.add(vc); writer.close(); }
private void rejectVariant(final VariantContext ctx, final String reason) { rejects.add(new VariantContextBuilder(ctx).filter(reason).make()); failedLiftover++; trackLiftedVariantContig(rejectsByContig, ctx.getContig()); }
@Override public Integer map(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) { if (tracker == null) return 0; final Collection<VariantContext> vcs = tracker.getValues(variantCollection.variants, context.getLocation()); for (VariantContext vc : vcs) { if (fullyDecode) vc = vc.fullyDecode(vcfRods.get(vc.getSource()), getToolkit().lenientVCFProcessing()); vcfWriter.add(vc); } return vcs.isEmpty() ? 0 : 1; }