Java SAMReadGroupRecord.setSample方法代码示例

import htsjdk.samtools.SAMReadGroupRecord; //导入方法依赖的package包/类
/**
 * setup read groups for the specified read groups and sample names
 *
 * @param header       the header to set
 * @param readGroupIDs the read group ID tags
 * @param sampleNames  the sample names
 * @return the adjusted SAMFileHeader
 */
public static SAMFileHeader createEnumeratedReadGroups(SAMFileHeader header, List<String> readGroupIDs, List<String> sampleNames) {
    if (readGroupIDs.size() != sampleNames.size()) {
        throw new ReviewedGATKException("read group count and sample name count must be the same");
    }

    List<SAMReadGroupRecord> readGroups = new ArrayList<SAMReadGroupRecord>();

    int x = 0;
    for (; x < readGroupIDs.size(); x++) {
        SAMReadGroupRecord rec = new SAMReadGroupRecord(readGroupIDs.get(x));
        rec.setSample(sampleNames.get(x));
        readGroups.add(rec);
    }
    header.setReadGroups(readGroups);
    return header;
}
 

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
/**
 * Build a SamFileWriter that will write its contents to the output file.
 *
 * @param output           The file to which to write
 * @param sampleAlias      The sample alias set in the read group header
 * @param libraryName      The name of the library to which this read group belongs
 * @param headerParameters Header parameters that will be added to the RG header for this SamFile
 * @return A SAMFileWriter
 */
private SAMFileWriterWrapper buildSamFileWriter(final File output, final String sampleAlias,
                                                final String libraryName, final Map<String, String> headerParameters,
                                                final boolean presorted) {
    IOUtil.assertFileIsWritable(output);
    final SAMReadGroupRecord rg = new SAMReadGroupRecord(READ_GROUP_ID);
    rg.setSample(sampleAlias);

    if (libraryName != null) rg.setLibrary(libraryName);
    for (final Map.Entry<String, String> tagNameToValue : headerParameters.entrySet()) {
        if (tagNameToValue.getValue() != null) {
            rg.setAttribute(tagNameToValue.getKey(), tagNameToValue.getValue());
        }
    }

    final SAMFileHeader header = new SAMFileHeader();

    header.setSortOrder(SAMFileHeader.SortOrder.queryname);
    header.addReadGroup(rg);
    return new SAMFileWriterWrapper(new SAMFileWriterFactory().makeSAMOrBAMWriter(header, presorted, output));
}
 

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
/**
 * Create a new HaplotypeBAMDestination
 *
 * @param sourceHeader SAMFileHeader used to seed the output SAMFileHeader for this destination.
 * @param haplotypeReadGroupID read group ID used when writing haplotypes as reads
 */
protected HaplotypeBAMDestination(SAMFileHeader sourceHeader, final String haplotypeReadGroupID) {
    Utils.nonNull(sourceHeader, "sourceHeader cannot be null");
    Utils.nonNull(haplotypeReadGroupID, "haplotypeReadGroupID cannot be null");
    this.haplotypeReadGroupID = haplotypeReadGroupID;

    bamOutputHeader = new SAMFileHeader();
    bamOutputHeader.setSequenceDictionary(sourceHeader.getSequenceDictionary());
    bamOutputHeader.setSortOrder(SAMFileHeader.SortOrder.coordinate);

    final List<SAMReadGroupRecord> readGroups = new ArrayList<>();
    readGroups.addAll(sourceHeader.getReadGroups()); // include the original read groups

    // plus an artificial read group for the haplotypes
    final SAMReadGroupRecord rgRec = new SAMReadGroupRecord(getHaplotypeReadGroupID());
    rgRec.setSample(haplotypeSampleTag);
    rgRec.setSequencingCenter("BI");
    readGroups.add(rgRec);
    bamOutputHeader.setReadGroups(readGroups);

    bamOutputHeader.addProgramRecord(new SAMProgramRecord("HalpotypeBAMWriter"));
}
 

import htsjdk.samtools.SAMReadGroupRecord; //导入方法依赖的package包/类
@DataProvider(name = "ReadsWithReadGroupData")
public Object[][] readsWithReadGroupData() {
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader(2, 1, 1000000);
    final SAMReadGroupRecord readGroup = new SAMReadGroupRecord("FOO");
    readGroup.setPlatform("FOOPLATFORM");
    readGroup.setPlatformUnit("FOOPLATFORMUNIT");
    readGroup.setLibrary("FOOLIBRARY");
    readGroup.setSample("FOOSAMPLE");
    header.addReadGroup(readGroup);

    final GATKRead googleBackedRead = new GoogleGenomicsReadToGATKReadAdapter(ArtificialReadUtils.createArtificialGoogleGenomicsRead("google", "1", 5, new byte[]{'A', 'C', 'G', 'T'}, new byte[]{1, 2, 3, 4}, "4M"));
    googleBackedRead.setReadGroup("FOO");

    final GATKRead samBackedRead = new SAMRecordToGATKReadAdapter(ArtificialReadUtils.createArtificialSAMRecord(header, "sam", header.getSequenceIndex("1"), 5, new byte[]{'A', 'C', 'G', 'T'}, new byte[]{1, 2, 3, 4}, "4M"));
    samBackedRead.setReadGroup("FOO");

    return new Object[][] {
            { googleBackedRead, header, "FOO" },
            { samBackedRead, header, "FOO" }
    };
}
 

import htsjdk.samtools.SAMReadGroupRecord; //导入方法依赖的package包/类
@Test
public void testGetSamplesFromHeader() {
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader(5, 1, 100);
    final List<SAMReadGroupRecord> readGroups = new ArrayList<>();
    for ( int i = 1; i <= 5; ++i ) {
        SAMReadGroupRecord readGroup = new SAMReadGroupRecord("ReadGroup" + i);
        readGroup.setSample("Sample" + i);
        readGroups.add(readGroup);
    }
    header.setReadGroups(readGroups);

    final Set<String> samples = ReadUtils.getSamplesFromHeader(header);
    Assert.assertEquals(samples.size(), 5, "Wrong number of samples returned from ReadUtils.getSamplesFromHeader()");
    for ( int i = 1; i <= 5; ++i ) {
        Assert.assertTrue(samples.contains("Sample" + i), "Missing Sample" + i + " in samples returned from ReadUtils.getSamplesFromHeader()");
    }
}
 

import htsjdk.samtools.SAMReadGroupRecord; //导入方法依赖的package包/类
public static SAMReadGroupRecord transfer(ReadGroupInfo readGroupInfo) {
    SAMReadGroupRecord record = new SAMReadGroupRecord(readGroupInfo.id());
    record.setSample(readGroupInfo.sample());
    record.setLibrary(readGroupInfo.lib());
    record.setPlatform(readGroupInfo.platform());
    record.setPlatformUnit(readGroupInfo.platformUnit());
    return record;
}
 

import htsjdk.samtools.SAMReadGroupRecord; //导入方法依赖的package包/类
/**
 * setup a default read group for a SAMFileHeader
 *
 * @param header      the header to set
 * @param readGroupID the read group ID tag
 * @param sampleName  the sample name
 * @return the adjusted SAMFileHeader
 */
public static SAMFileHeader createDefaultReadGroup(SAMFileHeader header, String readGroupID, String sampleName) {
    SAMReadGroupRecord rec = new SAMReadGroupRecord(readGroupID);
    rec.setSample(sampleName);
    List<SAMReadGroupRecord> readGroups = new ArrayList<SAMReadGroupRecord>();
    readGroups.add(rec);
    header.setReadGroups(readGroups);
    return header;
}
 

import htsjdk.samtools.SAMReadGroupRecord; //导入方法依赖的package包/类
@BeforeClass
public void setUp() {
    header = ArtificialReadUtils.createArtificialSamHeader(1, 1, 1000);
    rg = new SAMReadGroupRecord(RGID);
    rg.setSample(sample);
    header.addReadGroup(rg);
    parser = new GenomeLocParser(header.getSequenceDictionary());
}
 

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 testGetNoArgumentsReadGroup() throws Exception {
    final SAMReadGroupRecord expected = new SAMReadGroupRecord("RGID");
    expected.setProgramGroup("ReadTools");
    expected.setSample("sampleName");
    Assert.assertEquals(new ReadGroupArgumentCollection()
                    .getReadGroupFromArguments(expected.getReadGroupId(), expected.getSample()),
            expected);
}
 

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
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);
        }
    }
}
 

import htsjdk.samtools.SAMReadGroupRecord; //导入方法依赖的package包/类
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);
        }
    }
}