Java SAMReadGroupRecord.getSample方法代码示例

import htsjdk.samtools.SAMReadGroupRecord; //导入方法依赖的package包/类
/**
 * Pull out the sample names from a SAMFileHeader
 *
 * note that we use a TreeSet so that they are sorted
 *
 * @param header  the sam file header
 * @return list of strings representing the sample names
 */
public static Set<String> getSamplesFromHeader( final SAMFileHeader header ) {
    // get all of the unique sample names
    final Set<String> samples = new TreeSet<>();
    final List<SAMReadGroupRecord> readGroups = header.getReadGroups();

    for ( SAMReadGroupRecord readGroup : readGroups ) {
        final String sample = readGroup.getSample();
        if ( sample != null ) {
            samples.add(sample);
        }
    }

    return samples;
}
 

import htsjdk.samtools.SAMReadGroupRecord; //导入方法依赖的package包/类
public PicardAlignment(SAMRecord record) {
    super();

    this.record = record;

    this.flags = record.getFlags();

    String refName = record.getReferenceName();
    Genome genome = GenomeManager.getInstance().getCurrentGenome();
    this.chr = genome == null ? refName : genome.getCanonicalChrName(refName);

    // SAMRecord is 1 based inclusive.  IGV is 0 based exclusive.

    this.end = record.getAlignmentEnd();   // might be modified later for soft clipping
    this.start = record.getAlignmentStart() - 1;   // might be modified later for soft clipping


    if (record.getReadPairedFlag()) {
        String mateReferenceName = record.getMateReferenceName();
        String mateChr = genome == null ? mateReferenceName : genome.getCanonicalChrName(mateReferenceName);
        this.setMate(new ReadMate(mateChr,
                record.getMateAlignmentStart() - 1,
                record.getMateNegativeStrandFlag(),
                record.getMateUnmappedFlag()));
    }

    String keySequence = null;
    SAMFileHeader header = record.getHeader();
    String flowOrder = null;
    if (header != null) {
        readGroup = (String) record.getAttribute("RG");
        if (readGroup != null) {
            SAMReadGroupRecord rgRec = header.getReadGroup(readGroup);
            if (rgRec != null) {
                this.sample = rgRec.getSample();
                this.library = rgRec.getLibrary();
                flowOrder = rgRec.getFlowOrder();
                keySequence = rgRec.getKeySequence();
            }
        }
    }

    Object colorTag = record.getAttribute("YC");
    if (colorTag != null) {
        try {
            color = ColorUtilities.stringToColor(colorTag.toString(), null);
        } catch (Exception e) {
            log.error("Error interpreting color tag: " + colorTag, e);
        }
    }

    setPairOrientation();
    setPairStrands();
    createAlignmentBlocks(record.getCigarString(), record.getReadBases(), record.getBaseQualities(),
            getFlowSignals(flowOrder, keySequence), flowOrder, this.getFlowSignalsStart());


}
 

import htsjdk.samtools.SAMReadGroupRecord; //导入方法依赖的package包/类
public FingerprintIdDetails(final SAMReadGroupRecord rg, final String file) {
    this(rg.getPlatformUnit(), file);
    this.sample = rg.getSample();
    this.library = rg.getLibrary();
}
 

import htsjdk.samtools.SAMReadGroupRecord; //导入方法依赖的package包/类
@Override
protected String getKey(SAMReadGroupRecord rg) {
    return rg.getSample();
}
 

import htsjdk.samtools.SAMReadGroupRecord; //导入方法依赖的package包/类
/**
 * Returns the sample name associated with the provided read's read group.
 *
 * @param read read whose sample name to retrieve
 * @param header SAM header containing read groups
 * @return the sample name for the provided read's read group as a String,
 *         or null if the read has no read group.
 */
public static String getSampleName( final GATKRead read, final SAMFileHeader header ) {
    final SAMReadGroupRecord readGroup = getSAMReadGroupRecord(read, header);
    return readGroup != null ? readGroup.getSample() : null;
}