protected ReadDestination(final SAMFileHeader header, final String readGroupID) { // prepare the bam header if (header == null) throw new IllegalArgumentException("header cannot be null"); bamHeader = new SAMFileHeader(); bamHeader.setSequenceDictionary(header.getSequenceDictionary()); bamHeader.setSortOrder(SAMFileHeader.SortOrder.coordinate); // include the original read groups plus a new artificial one for the haplotypes final List<SAMReadGroupRecord> readGroups = new ArrayList<SAMReadGroupRecord>(header.getReadGroups()); final SAMReadGroupRecord rg = new SAMReadGroupRecord(readGroupID); rg.setSample("HC"); rg.setSequencingCenter("BI"); readGroups.add(rg); bamHeader.setReadGroups(readGroups); }
protected int doWork() { IoUtil.assertFileIsReadable(INPUT); IoUtil.assertFileIsWritable(OUTPUT); final SAMFileReader in = new SAMFileReader(INPUT); // create the read group we'll be using final SAMReadGroupRecord rg = new SAMReadGroupRecord(RGID); rg.setLibrary(RGLB); rg.setPlatform(RGPL); rg.setSample(RGSM); rg.setPlatformUnit(RGPU); if (RGCN != null) rg.setSequencingCenter(RGCN); if (RGDS != null) rg.setDescription(RGDS); if (RGDT != null) rg.setRunDate(RGDT); log.info( String.format( "Created read group ID=%s PL=%s LB=%s SM=%s%n", rg.getId(), rg.getPlatform(), rg.getLibrary(), rg.getSample())); // create the new header and output file final SAMFileHeader inHeader = in.getFileHeader(); final SAMFileHeader outHeader = inHeader.clone(); outHeader.setReadGroups(Arrays.asList(rg)); if (SORT_ORDER != null) outHeader.setSortOrder(SORT_ORDER); final SAMFileWriter outWriter = new SAMFileWriterFactory() .makeSAMOrBAMWriter( outHeader, outHeader.getSortOrder() == inHeader.getSortOrder(), OUTPUT); final ProgressLogger progress = new ProgressLogger(log); for (final SAMRecord read : in) { read.setAttribute(SAMTag.RG.name(), RGID); outWriter.addAlignment(read); progress.record(read); } // cleanup in.close(); outWriter.close(); return 0; }
@BeforeClass private void init() throws IOException { reference = new CachingIndexedFastaSequenceFile(new File(b37KGReference)); dictionary = reference.getSequenceDictionary(); genomeLocParser = new GenomeLocParser(dictionary); header = ArtificialSAMUtils.createDefaultReadGroup(new SAMFileHeader(), "test", "test"); header.setSequenceDictionary(dictionary); header.setSortOrder(SAMFileHeader.SortOrder.coordinate); readGroup = new GATKSAMReadGroupRecord(header.getReadGroup("test")); final List<GATKSAMRecord> reads = new ArrayList<>(); for (final String contig : contigs) { for (int i = 1; i <= numReadsPerContig; i++) { reads.add(buildSAMRecord("read" + contig + "_" + i, contig, i)); } } createBAM(reads); }