Java Code Examples for htsjdk.samtools.SAMReadGroupRecord#setLibrary()

The following examples show how to use htsjdk.samtools.SAMReadGroupRecord#setLibrary() . You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may check out the related API usage on the sidebar.
Example 1
Source File: FastqToSam.java    From picard with MIT License 6 votes vote down vote up 
/** 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 ;
}
Example 2
Source File: FingerprintChecker.java    From picard with MIT License 6 votes vote down vote up 
private FingerprintIdDetails createUnknownFP(final Path samFile, final SAMRecord rec) {
    final PicardException e = new PicardException("Found read with no readgroup: " + rec.getReadName() + " in file: " + samFile);
    if (validationStringency != ValidationStringency.STRICT) {
        final SAMReadGroupRecord readGroupRecord = new SAMReadGroupRecord("<UNKNOWN>:::" + samFile.toUri().toString());
        readGroupRecord.setLibrary("<UNKNOWN>");
        readGroupRecord.setSample(defaultSampleID);
        readGroupRecord.setPlatformUnit("<UNKNOWN>.0.ZZZ");

        if (validationStringency != ValidationStringency.SILENT && missingRGFiles.add(samFile)) {
            log.warn(e.getMessage());
            log.warn("further messages from this file will be suppressed");
        }

        return new FingerprintIdDetails(readGroupRecord, samFile.toUri().toString());
    } else {
        log.error(e.getMessage());
        throw e;
    }
}
Example 3
Source File: HalvadeReducer.java    From halvade with GNU General Public License v3.0 6 votes vote down vote up 
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;
}
Example 4
Source File: SingleCellRnaSeqMetricsCollector.java    From Drop-seq with MIT License 5 votes vote down vote up 
public List<SAMReadGroupRecord> getReadGroups(final List<String> cellBarcodes) {
	List<SAMReadGroupRecord> g = new ArrayList<>(cellBarcodes.size());
	for (String id: cellBarcodes) {
		SAMReadGroupRecord rg = new SAMReadGroupRecord(id);
		rg.setLibrary(id);
	    rg.setPlatform(id);
	    rg.setSample(id);
	    rg.setPlatformUnit(id);
		g.add(rg);
	}
	return (g);
}
Example 5
Source File: CollectGcBiasMetricsTest.java    From picard with MIT License 5 votes vote down vote up 
public void setupTest1(final int ID, final String readGroupId, final SAMReadGroupRecord readGroupRecord, final String sample,
                  final String library, final SAMFileHeader header, final SAMRecordSetBuilder setBuilder)
        throws IOException {

    final String separator = ":";
    final int contig1 = 0;
    final int contig2 = 1;
    readGroupRecord.setSample(sample);
    readGroupRecord.setPlatform(platform);
    readGroupRecord.setLibrary(library);
    readGroupRecord.setPlatformUnit(readGroupId);
    header.addReadGroup(readGroupRecord);
    setBuilder.setReadGroup(readGroupRecord);
    setBuilder.setUseNmFlag(true);

    setBuilder.setHeader(header);

    final int max = 800;
    final int min = 1;
    final Random rg = new Random(5);

    //add records that align to chrM and O but not N
    for (int i = 0; i < NUM_READS; i++) {
        final int start = rg.nextInt(max) + min;
        final String newReadName = READ_NAME + separator + ID + separator + i;

        if (i != NUM_READS - 1) {
            setBuilder.addPair(newReadName, contig1, start + ID, start + ID + LENGTH);
        } else {
            setBuilder.addPair(newReadName, contig2, start + ID, start + ID + LENGTH);
        }
    }
}
Example 6
Source File: CollectGcBiasMetricsTest.java    From picard with MIT License 5 votes vote down vote up 
public void setupTest2(final int ID, final String readGroupId, final SAMReadGroupRecord readGroupRecord, final String sample,
                       final String library, final SAMFileHeader header, final SAMRecordSetBuilder setBuilder)
        throws IOException {

    final String separator = ":";
    final int contig1 = 0;
    final int contig2 = 1;
    final int contig3 = 2;
    readGroupRecord.setSample(sample);
    readGroupRecord.setPlatform(platform);
    readGroupRecord.setLibrary(library);
    readGroupRecord.setPlatformUnit(readGroupId);
    setBuilder.setReadGroup(readGroupRecord);
    setBuilder.setUseNmFlag(true);

    setBuilder.setHeader(header);

    final int max = 800;
    final int min = 1;
    final Random rg = new Random(5);

    //add records that align to all 3 chr in reference file
    for (int i = 0; i < NUM_READS; i++) {
        final int start = rg.nextInt(max) + min;
        final String newReadName = READ_NAME + separator + ID + separator + i;

        if (i<=NUM_READS/3) {
            setBuilder.addPair(newReadName, contig1, start + ID, start + ID + LENGTH);
        } else if (i< (NUM_READS - (NUM_READS/3))) {
            setBuilder.addPair(newReadName, contig2, start + ID, start + ID + LENGTH);
        } else {
            setBuilder.addPair(newReadName, contig3, start + ID, start + ID + LENGTH);
        }
    }
}
Example 7
Source File: CollectMultipleMetricsTest.java    From picard with MIT License 5 votes vote down vote up 
void setup(final int numReads,
           final String readName,
           final int ID,
           final String readGroupId,
           final SAMReadGroupRecord readGroupRecord,
           final String sample,
           final String library,
           final SAMFileHeader header,
           final SAMRecordSetBuilder setBuilder) throws IOException {
    final String separator = ":";
    readGroupRecord.setSample(sample);
    readGroupRecord.setPlatform(platform);
    readGroupRecord.setLibrary(library);
    readGroupRecord.setPlatformUnit(readGroupId);
    header.addReadGroup(readGroupRecord);
    setBuilder.setReadGroup(readGroupRecord);
    setBuilder.setUseNmFlag(true);
    setBuilder.setHeader(header);

    final int max = 15000;
    final int min = 1;
    final Random rg = new Random(5);

    for (int i = 0; i < numReads; i++) {
        final int start = rg.nextInt(max) + min;
        final String newReadName = readName + separator + ID + separator + i;
        setBuilder.addPair(newReadName, 0, start + ID, start + ID + 99);
    }
}
Example 8
Source File: AddOrReplaceReadGroups.java    From picard with MIT License 4 votes vote down vote up 
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;
}
Example 9
Source File: ReadsKeyUnitTest.java    From gatk with BSD 3-Clause "New" or "Revised" License 4 votes vote down vote up 
@DataProvider
public Object[][] artificalReadsForKeys() {
    SAMReadGroupRecord library1 = new SAMReadGroupRecord("rg1");
    library1.setLibrary("library1");
    SAMReadGroupRecord library2 = new SAMReadGroupRecord("rg2");
    library2.setLibrary("library2");

    SAMFileHeader header = hg19Header.clone();
    header.addReadGroup(library1);
    header.addReadGroup(library2);

    return new Object[][]{
            // Test of two groups with different start positions
            {header, createTestRead("name1", "1", 1000, "100M", library1.getReadGroupId(), false),
                    createTestRead("name1", "1", 1200, "100M", library1.getReadGroupId(), true),
                    false,
                    createTestRead("name2", "1", 1010, "100M", library1.getReadGroupId(), false),
                    createTestRead("name2", "1", 1200, "100M", library1.getReadGroupId(), true),},

            // Test of two equivalent groups
            {header, createTestRead("name1", "1", 1000, "100M", library1.getReadGroupId(), false),
                    createTestRead("name1", "1", 1200, "100M", library1.getReadGroupId(), true),
                    true,
                    createTestRead("name2", "1", 1000, "100M", library1.getReadGroupId(), false),
                    createTestRead("name2", "1", 1200, "100M", library1.getReadGroupId(), true),},

            // Test of two equivalent group, different contig
            {header, createTestRead("name1", "1", 1000, "100M", library1.getReadGroupId(), false),
                    createTestRead("name1", "1", 1200, "100M", library1.getReadGroupId(), true),
                    false,
                    createTestRead("name2", "2", 1000, "100M", library1.getReadGroupId(), false),
                    createTestRead("name2", "2", 1200, "100M", library1.getReadGroupId(), true),},

            // Test of two equivalent groups, different orientation
            {header, createTestRead("name1", "1", 1000, "100M", library1.getReadGroupId(), false),
                    createTestRead("name1", "1", 1200, "100M", library1.getReadGroupId(), true),
                    false,
                    createTestRead("name2", "1", 1000, "100M", library1.getReadGroupId(), true),
                    createTestRead("name2", "1", 1200, "100M", library1.getReadGroupId(), true),},

            // Test of two equivalent grops, but different libraries
            {header, createTestRead("name1", "1", 1000, "100M", library1.getReadGroupId(), false),
                    createTestRead("name1", "1", 1200, "100M", library1.getReadGroupId(), true),
                    false,
                    createTestRead("name2", "1", 1000, "100M", library2.getReadGroupId(), false),
                    createTestRead("name2", "1", 1200, "100M", library2.getReadGroupId(), true),},

            // Test of two equivalent groups, but one was soft-clipped to a different start
            {header, createTestRead("name1", "1", 1010, "10S90M", library1.getReadGroupId(), false),
                    createTestRead("name1", "1", 1200, "100M", library1.getReadGroupId(), true),
                    true,
                    createTestRead("name2", "1", 1000, "100M", library1.getReadGroupId(), false),
                    createTestRead("name2", "1", 1200, "100M", library1.getReadGroupId(), true),},

            // Test of two equivalent groups, but one read is on a different contig
            {header, createTestRead("name1", "1", 1000, "100M", library1.getReadGroupId(), false),
                    createTestRead("name1", "1", 1200, "100M", library1.getReadGroupId(), true),
                    false,
                    createTestRead("name2", "1", 1000, "100M", library1.getReadGroupId(), false),
                    createTestRead("name2", "2", 1200, "100M", library1.getReadGroupId(), true),},

    };
}