Package org.broadinstitute.gatk.utils.sam

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

409
410
411
412
413
414
415
416
417
418
419
420
421
422
        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());
View Full Code Here
TOP

Related Classes of org.broadinstitute.gatk.utils.sam.NWaySAMFileWriter

  • org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID
  • org.broadinstitute.gatk.tools.walkers.indels.IndelRealigner
  • java.io.File
  • org.broadinstitute.gatk.utils.exceptions.GATKException
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.