Java SAMReadGroupRecord.setPredictedMedianInsertSize方法代码示例

import htsjdk.samtools.SAMReadGroupRecord; //导入方法依赖的package包/类
protected SAMReadGroupRecord createReadGroupRecord(
        String RGID, String RGLB, String RGPL, 
        String RGPU, String RGSM, String RGCN, 
        String RGDS, Iso8601Date RGDT, Integer RGPI) {
    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);
    if(RGPI != null)
        rg.setPredictedMedianInsertSize(RGPI);
    return rg;
}
 

import htsjdk.samtools.SAMReadGroupRecord; //导入方法依赖的package包/类
/** Creates a simple header with the values provided on the command line. */
public SAMFileHeader createSamFileHeader() {
    final SAMReadGroupRecord rgroup = new SAMReadGroupRecord(this.READ_GROUP_NAME);
    rgroup.setSample(this.SAMPLE_NAME);
    if (this.LIBRARY_NAME != null) rgroup.setLibrary(this.LIBRARY_NAME);
    if (this.PLATFORM != null) rgroup.setPlatform(this.PLATFORM);
    if (this.PLATFORM_UNIT != null) rgroup.setPlatformUnit(this.PLATFORM_UNIT);
    if (this.SEQUENCING_CENTER != null) rgroup.setSequencingCenter(SEQUENCING_CENTER);
    if (this.PREDICTED_INSERT_SIZE != null) rgroup.setPredictedMedianInsertSize(PREDICTED_INSERT_SIZE);
    if (this.DESCRIPTION != null) rgroup.setDescription(this.DESCRIPTION);
    if (this.RUN_DATE != null) rgroup.setRunDate(this.RUN_DATE);
    if (this.PLATFORM_MODEL != null) rgroup.setPlatformModel(this.PLATFORM_MODEL);
    if (this.PROGRAM_GROUP != null) rgroup.setProgramGroup(this.PROGRAM_GROUP);

    final SAMFileHeader header = new SAMFileHeader();
    header.addReadGroup(rgroup);

    for (final String comment : COMMENT) {
        header.addComment(comment);
    }

    header.setSortOrder(this.SORT_ORDER);
    return header ;
}
 

import htsjdk.samtools.SAMReadGroupRecord; //导入方法依赖的package包/类
/**
 * Gets a basic Read Group from the arguments.
 *
 * Note: the program group is set to {@link RTHelpConstants#PROGRAM_NAME}.
 *
 */
public SAMReadGroupRecord getReadGroupFromArguments(final String id, final String sampleName) {
    final SAMReadGroupRecord rg = new SAMReadGroupRecord(id);
    rg.setProgramGroup(RTHelpConstants.PROGRAM_NAME);
    rg.setSample(sampleName);
    // the program group is the one in the project properties
    rg.setProgramGroup(RTHelpConstants.PROGRAM_NAME);
    if (readGroupLibrary != null) {
        rg.setLibrary(readGroupLibrary);
    }
    if (readGroupPlatform != null) {
        rg.setPlatform(readGroupPlatform.toString());
    }
    if (readGroupPlatformUnit != null) {
        rg.setPlatformUnit(readGroupPlatformUnit);
    }
    if (readGroupSequencingCenter != null) {
        rg.setSequencingCenter(readGroupSequencingCenter);
    }
    if (readGroupRunDate != null) {
        rg.setRunDate(readGroupRunDate);
    }
    if (readGroupPredictedInsertSize != null) {
        rg.setPredictedMedianInsertSize(readGroupPredictedInsertSize);
    }
    if (readGroupPlatformModel != null) {
        rg.setPlatformModel(readGroupPlatformModel);
    }
    // return it
    return rg;
}
 

import htsjdk.samtools.SAMReadGroupRecord; //导入方法依赖的package包/类
@Test
public void testGetReadGroupWithArguments() throws Exception {
    // setting expected RG
    final SAMReadGroupRecord expected = new SAMReadGroupRecord("RGID");
    expected.setProgramGroup("ReadTools");
    expected.setSample("sampleName");
    // setting args
    final ReadGroupArgumentCollection rgargs = new ReadGroupArgumentCollection();

    // starting setting params
    expected.setLibrary("LB");
    rgargs.readGroupLibrary = "LB";

    expected.setPlatform("ILLUMINA");
    rgargs.readGroupPlatform = SAMReadGroupRecord.PlatformValue.ILLUMINA;

    expected.setPlatformUnit("PU");
    rgargs.readGroupPlatformUnit = expected.getPlatformUnit();

    expected.setSequencingCenter("CN");
    rgargs.readGroupSequencingCenter = expected.getSequencingCenter();

    final Iso8601Date date = new Iso8601Date("2007-11-03");
    expected.setRunDate(date);
    rgargs.readGroupRunDate = date;

    expected.setPredictedMedianInsertSize(100);
    rgargs.readGroupPredictedInsertSize = expected.getPredictedMedianInsertSize();

    expected.setPlatformModel("PM");
    rgargs.readGroupPlatformModel = expected.getPlatformModel();

    // testing
    Assert.assertEquals(rgargs
                    .getReadGroupFromArguments(expected.getReadGroupId(), expected.getSample()),
            expected);
}
 

import htsjdk.samtools.SAMReadGroupRecord; //导入方法依赖的package包/类
protected int doWork() {
    IOUtil.assertInputIsValid(INPUT);
    IOUtil.assertFileIsWritable(OUTPUT);

    final SamReader in = SamReaderFactory.makeDefault()
        .referenceSequence(REFERENCE_SEQUENCE)
        .open(SamInputResource.of(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);
    if (RGPI != null) rg.setPredictedMedianInsertSize(RGPI);
    if (RGPG != null) rg.setProgramGroup(RGPG);
    if (RGPM != null) rg.setPlatformModel(RGPM);
    if (RGKS != null) rg.setKeySequence(RGKS);
    if (RGFO != null) rg.setFlowOrder(RGFO);

    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(Collections.singletonList(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
    CloserUtil.close(in);
    outWriter.close();
    return 0;
}