/** * Create VCFHeaderLines for each refDict entry, and optionally the assembly if referenceFile != null * @param refDict reference dictionary * @param referenceFile for assembly name. May be null * @return list of vcf contig header lines */ public static List<VCFContigHeaderLine> makeContigHeaderLines(final SAMSequenceDictionary refDict, final File referenceFile) { final List<VCFContigHeaderLine> lines = new ArrayList<VCFContigHeaderLine>(); final String assembly = referenceFile != null ? getReferenceAssembly(referenceFile.getName()) : null; for ( SAMSequenceRecord contig : refDict.getSequences() ) lines.add(makeContigHeaderLine(contig, assembly)); return lines; }
/** * Create VCFHeaderLines for each refDict entry, and optionally the assembly if referenceFile != null * * @param refDict reference dictionary * @param referenceFile for assembly name. May be null * @return list of vcf contig header lines */ public static List<VCFContigHeaderLine> makeContigHeaderLines(final SAMSequenceDictionary refDict, final File referenceFile) { final List<VCFContigHeaderLine> lines = new ArrayList<>(); final String assembly = referenceFile != null ? getReferenceAssembly(referenceFile.getName()) : null; for (final SAMSequenceRecord contig : refDict.getSequences()) lines.add(makeContigHeaderLine(contig, assembly)); return lines; }
/** * Create VCFHeaderLines for each refDict entry, and optionally the assembly if referenceFile != null * * @param refDict reference dictionary * @param referenceFile for assembly name. May be null * @return list of vcf contig header lines */ public static List<VCFContigHeaderLine> makeContigHeaderLines(final SAMSequenceDictionary refDict, final File referenceFile) { final List<VCFContigHeaderLine> lines = new ArrayList<>(); final String assembly = referenceFile != null ? getReferenceAssembly(referenceFile.getName()) : null; for (final SAMSequenceRecord contig : refDict.getSequences()) lines.add(makeContigHeaderLine(contig, assembly)); return lines; }