public boolean isLazyWithData() { return this instanceof LazyGenotypesContext && ((LazyGenotypesContext)this).getUnparsedGenotypeData() != null; }
public boolean isLazyWithData() { return this instanceof LazyGenotypesContext && ((LazyGenotypesContext)this).getUnparsedGenotypeData() != null; }
public boolean isLazyWithData() { return this instanceof LazyGenotypesContext && ((LazyGenotypesContext)this).getUnparsedGenotypeData() != null; }
private BCF2Codec.LazyData getLazyData(final VariantContext vc) { if ( vc.getGenotypes().isLazyWithData() ) { final LazyGenotypesContext lgc = (LazyGenotypesContext)vc.getGenotypes(); if ( lgc.getUnparsedGenotypeData() instanceof BCF2Codec.LazyData && canSafelyWriteRawGenotypesBytes((BCF2Codec.LazyData) lgc.getUnparsedGenotypeData())) { return (BCF2Codec.LazyData)lgc.getUnparsedGenotypeData(); } else { lgc.decode(); // WARNING -- required to avoid keeping around bad lazy data for too long } } return null; }
private BCF2Codec.LazyData getLazyData(final VariantContext vc) { if ( vc.getGenotypes().isLazyWithData() ) { final LazyGenotypesContext lgc = (LazyGenotypesContext)vc.getGenotypes(); if ( lgc.getUnparsedGenotypeData() instanceof BCF2Codec.LazyData && canSafelyWriteRawGenotypesBytes((BCF2Codec.LazyData) lgc.getUnparsedGenotypeData())) { return (BCF2Codec.LazyData)lgc.getUnparsedGenotypeData(); } else { lgc.decode(); // WARNING -- required to avoid keeping around bad lazy data for too long } } return null; }
private BCF2Codec.LazyData getLazyData(final VariantContext vc) { if ( vc.getGenotypes().isLazyWithData() ) { final LazyGenotypesContext lgc = (LazyGenotypesContext)vc.getGenotypes(); if ( lgc.getUnparsedGenotypeData() instanceof BCF2Codec.LazyData && canSafelyWriteRawGenotypesBytes((BCF2Codec.LazyData) lgc.getUnparsedGenotypeData())) { return (BCF2Codec.LazyData)lgc.getUnparsedGenotypeData(); } else { lgc.decode(); // WARNING -- required to avoid keeping around bad lazy data for too long } } return null; }
private String toStringUnparsedGenotypes() { return String.format("[VC %s @ %s Q%s of type=%s alleles=%s attr=%s GT=%s filters=%s", getSource(), contig + ":" + (start - stop == 0 ? start : start + "-" + stop), hasLog10PError() ? String.format("%.2f", getPhredScaledQual()) : ".", this.getType(), ParsingUtils.sortList(this.getAlleles()), ParsingUtils.sortedString(this.getAttributes()), ((LazyGenotypesContext)this.genotypes).getUnparsedGenotypeData(), String.join(",", commonInfo.getFilters())); }
private String toStringUnparsedGenotypes() { return String.format("[VC %s @ %s Q%s of type=%s alleles=%s attr=%s GT=%s filters=%s", getSource(), contig + ":" + (start - stop == 0 ? start : start + "-" + stop), hasLog10PError() ? String.format("%.2f", getPhredScaledQual()) : ".", this.getType(), ParsingUtils.sortList(this.getAlleles()), ParsingUtils.sortedString(this.getAttributes()), ((LazyGenotypesContext)this.genotypes).getUnparsedGenotypeData(), String.join(",", commonInfo.getFilters())); }
private String toStringUnparsedGenotypes() { return String.format("[VC %s @ %s Q%s of type=%s alleles=%s attr=%s GT=%s", getSource(), contig + ":" + (start - stop == 0 ? start : start + "-" + stop), hasLog10PError() ? String.format("%.2f", getPhredScaledQual()) : ".", this.getType(), ParsingUtils.sortList(this.getAlleles()), ParsingUtils.sortedString(this.getAttributes()), ((LazyGenotypesContext)this.genotypes).getUnparsedGenotypeData()); }
if (gc.isLazyWithData() && ((LazyGenotypesContext) gc).getUnparsedGenotypeData() instanceof String) { stringBuilder.append(VCFConstants.FIELD_SEPARATOR); stringBuilder.append(((LazyGenotypesContext) gc).getUnparsedGenotypeData().toString()); } else { final List<String> genotypeAttributeKeys = context.calcVCFGenotypeKeys(this.header);
vc.getGenotypes(); genotypesData = gc.getUnparsedGenotypeData(); numGenotypes = gc.size();
vc.getGenotypes(); genotypesData = gc.getUnparsedGenotypeData(); numGenotypes = gc.size();
vc.getGenotypes(); genotypesData = gc.getUnparsedGenotypeData(); numGenotypes = gc.size();
if (gc.isLazyWithData() && ((LazyGenotypesContext) gc).getUnparsedGenotypeData() instanceof String) { vcfOutput.append(VCFConstants.FIELD_SEPARATOR); vcfOutput.append(((LazyGenotypesContext) gc).getUnparsedGenotypeData().toString()); } else { final List<String> genotypeAttributeKeys = context.calcVCFGenotypeKeys(this.header);
if (gc.isLazyWithData() && ((LazyGenotypesContext) gc).getUnparsedGenotypeData() instanceof String) { vcfOutput.append(VCFConstants.FIELD_SEPARATOR); vcfOutput.append(((LazyGenotypesContext) gc).getUnparsedGenotypeData().toString()); } else { final List<String> genotypeAttributeKeys = context.calcVCFGenotypeKeys(this.header);