Examples of htsjdk.samtools.SAMFileReader.query()

        SAMRecordIterator rawIterator;
        if ( location == null )
            rawIterator = reader.iterator();
        else {
            final GenomeLoc loc = genomeLocParser.parseGenomeLoc(location);
            rawIterator = reader.query(loc.getContig(), loc.getStart(), loc.getStop(), false);
        }


        final GATKSAMRecordIterator iterator = new GATKSAMRecordIterator(rawIterator);


        final Set<String> samples = new HashSet<String>();

        if (in.hasIndex()) {
            final SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(outHeader, true, OUTPUT);


            // write the reads in contig order
            for (final SAMSequenceRecord contig : refDict.getSequences() ) {
                final SAMRecordIterator it = in.query(contig.getSequenceName(), 0, 0, false);
                writeReads(out, it, newOrder, contig.getSequenceName());
            }
            // don't forget the unmapped reads
            writeReads( out, in.queryUnmapped(), newOrder, "unmapped" );
            out.close();

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