Examples with VCFContigHeaderLine htsjdk.variant.vcf.VCFContigHeaderLine used on opensource projects

Example 6 with VCFContigHeaderLine

use of htsjdk.variant.vcf.VCFContigHeaderLine in project jvarkit by lindenb.

the class VCFUtils method samSequenceDictToVCFContigHeaderLine.

public static SortedSet<VCFContigHeaderLine> samSequenceDictToVCFContigHeaderLine(SAMSequenceDictionary dict) {
    SortedSet<VCFContigHeaderLine> meta2 = new TreeSet<VCFContigHeaderLine>();
    for (SAMSequenceRecord ssr : dict.getSequences()) {
        Map<String, String> mapping = new HashMap<String, String>();
        mapping.put("ID", ssr.getSequenceName());
        mapping.put("length", String.valueOf(ssr.getSequenceLength()));
        String as = ssr.getAssembly();
        if (as != null && !as.trim().isEmpty())
            mapping.put("assembly", as);
        VCFContigHeaderLine h = new VCFContigHeaderLine(mapping, ssr.getSequenceIndex());
        meta2.add(h);
    }
    return meta2;
}