final int CA_GENBANK_ACCESSION = 3; for (ImmutableList<String> line : accessionLines) { builder.putContigID(line.get(CA_CHROMOSOME), chrID); // e.g. "1", "X" builder.putContigID("chr" + line.get(CA_CHROMOSOME), chrID); // e.g. "chr1", "chrX", for UCSC builder.putContigID(line.get(CA_REFSEQ_ACCESSION), chrID); // e.g. "NC_000001.10" builder.putContigID(line.get(CA_GENBANK_ACCESSION), chrID); // e.g. "CM000663.1" chrID += 1; if (!line.get(line.size() - 1).equals(filterPattern)) continue; // skip, does not match builder.putContigID(line.get(CA_CHROMOSOME), chrID); // e.g. "1", "X" builder.putContigID("chr" + line.get(CA_CHROMOSOME), chrID); // e.g. "chr1", "chrX", for UCSC builder.putContigID(line.get(CA_REFSEQ_ACCESSION), chrID); // e.g. "NC_000001.10" chrID += 1; if (builder.getContigID(fields[0]) == null) { builder.putContigName(chrID, fields[0]); builder.putContigID(fields[0], chrID); if (!fields[0].startsWith("chr")) builder.putContigID("chr" + fields[0], chrID++); builder.putContigID(fields[j], builder.getContigID(fields[0])); if (!fields[j].startsWith("chr")) builder.putContigID("chr" + fields[j], builder.getContigID(fields[0]));
builder.putContigID("" + i, i); builder.putContigID("chr" + i, i); builder.putContigID("X", 23); builder.putContigName(24, "Y"); builder.putContigID("Y", 24); builder.putContigName(25, "M"); builder.putContigID("M", 25); builder.putContigID("chrX", 23); builder.putContigID("chrY", 24); builder.putContigID("chrM", 25);