Examples of NWaySAMFileWriter


Examples of org.broadinstitute.gatk.utils.sam.NWaySAMFileWriter

        if ( N_WAY_OUT != null ) {
            boolean createIndex =  true;

            if ( N_WAY_OUT.toUpperCase().endsWith(".MAP") ) {
                writerToUse = new NWaySAMFileWriter(getToolkit(),loadFileNameMap(N_WAY_OUT),
                            SAMFileHeader.SortOrder.coordinate,true, createIndex, generateMD5s,createProgramRecord(),KEEP_ALL_PG_RECORDS);
            } else {
                writerToUse = new NWaySAMFileWriter(getToolkit(),N_WAY_OUT,SAMFileHeader.SortOrder.coordinate,true,
                        createIndex, generateMD5s,createProgramRecord(),KEEP_ALL_PG_RECORDS);
            }
        }   else {
            // set up the output writer
            setupWriter(getToolkit().getSAMFileHeader());
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