Examples of SAMReadGroupRecord

Examples of htsjdk.samtools.SAMReadGroupRecord

                    new File(OUTPUT, IOUtil.makeFileNameSafe(lib) + extension)));
        }


        for (Iterator<SAMRecord> it = reader.iterator(); it.hasNext(); ) {
            SAMRecord sam = it.next();
            SAMReadGroupRecord rg = sam.getReadGroup();
            if (rg != null && rg.getLibrary() != null) {
                libraryToWriter.get(rg.getLibrary()).addAlignment(sam);
            }
            else {
                if (unknown == null) {
                    unknown = factory.makeSAMOrBAMWriter(unknownHeader, true,
                            new File(OUTPUT, "unknown" + extension));

View Full Code Here

Examples of htsjdk.samtools.SAMReadGroupRecord

        Assert.assertEquals(pg.getProgramGroupId(), "0");
        Assert.assertEquals(pg.getProgramVersion(), "1.0");
        Assert.assertEquals(pg.getCommandLine(), "align!");
        Assert.assertEquals(pg.getProgramName(), "myAligner");


        final SAMReadGroupRecord rg = result.getFileHeader().getReadGroups().get(0);
        Assert.assertEquals(rg.getReadGroupId(), "0");
        Assert.assertEquals(rg.getSample(), "Hi,Mom!");


        Assert.assertEquals(result.getFileHeader().getSortOrder(), SAMFileHeader.SortOrder.coordinate);


        for (final SAMRecord sam : result) {
            // This tests that we clip both (a) when the adapter is marked in the unmapped BAM file and

View Full Code Here

Examples of htsjdk.samtools.SAMReadGroupRecord

     */
    public static String getLibraryName(final SAMFileHeader header, final SAMRecord rec) {
        final String readGroupId = (String) rec.getAttribute("RG");


        if (readGroupId != null) {
            final SAMReadGroupRecord rg = header.getReadGroup(readGroupId);
            if (rg != null) {
                final String libraryName = rg.getLibrary();
                if (null != libraryName) return libraryName;
            }
        }


        return "Unknown Library";

View Full Code Here

Examples of htsjdk.samtools.SAMReadGroupRecord

        // Create some alignments that hit the ribosomal sequence, various parts of the gene, and intergenic.
        final SAMRecordSetBuilder builder = new SAMRecordSetBuilder(true, SAMFileHeader.SortOrder.coordinate, false);
        // Set seed so that strandedness is consistent among runs.
        builder.setRandomSeed(0);
        final int sequenceIndex = builder.getHeader().getSequenceIndex(sequence);
        final SAMReadGroupRecord rg1 = new SAMReadGroupRecord("2");
        rg1.setSample("Sample");
        rg1.setLibrary("foo");
        builder.setReadGroup(rg1);
        builder.addPair("pair1", sequenceIndex, 45, 475);
        builder.addPair("pair2", sequenceIndex, 90, 225);
        builder.addFrag("frag1", sequenceIndex, 150, true);
        builder.addFrag("frag2", sequenceIndex, 450, true);


        final SAMReadGroupRecord rg2 = new SAMReadGroupRecord("3");
        rg2.setSample("Sample");
        rg2.setLibrary("bar");
        builder.setReadGroup(rg2);
        builder.addPair("pair3", sequenceIndex, 120, 600);
        builder.addFrag("frag3", sequenceIndex, 225, false);
        builder.addPair("rrnaPair", sequenceIndex, 400, 500);

View Full Code Here

Examples of net.sf.samtools.SAMReadGroupRecord

  public Sam2CramRecordFactory(byte[] refBases, SAMFileHeader samFileHeader) {
    this.refBases = refBases;


    List<SAMReadGroupRecord> readGroups = samFileHeader.getReadGroups();
    for (int i = 0; i < readGroups.size(); i++) {
      SAMReadGroupRecord readGroupRecord = readGroups.get(i);
      readGroupMap.put(readGroupRecord.getId(), i);
    }
  }

View Full Code Here

Examples of net.sf.samtools.SAMReadGroupRecord

    cramRecord.setMappingQuality(record.getMappingQuality());
    cramRecord.setDuplicate(record.getDuplicateReadFlag());


    cramRecord.templateSize = record.getInferredInsertSize();


    SAMReadGroupRecord readGroup = record.getReadGroup();
    Integer rgIndex = 0;
    if (readGroup != null)
//      rgIndex = readGroupMap.get(readGroup.getId());
      cramRecord.setReadGroupID(readGroupMap.get(readGroup.getId()));
    else
      cramRecord.setReadGroupID(-1);
//      rgIndex = readGroupMap.get(UNKNOWN_READ_GROUP_ID);


//    if (rgIndex == null)

View Full Code Here

Examples of net.sf.samtools.SAMReadGroupRecord

      for (ReadTag tag : cramRecord.tags)
        samRecord.setAttribute(tag.getKey(), tag.getValue());


    if (cramRecord.getReadGroupID() > -1) {
//    if (cramRecord.getReadGroupID() < header.getReadGroups().size()) {
      SAMReadGroupRecord readGroupRecord = header.getReadGroups().get(
          cramRecord.getReadGroupID());
      samRecord.setAttribute("RG", readGroupRecord.getId());
    }


    return samRecord;
  }

View Full Code Here

Examples of net.sf.samtools.SAMReadGroupRecord

            firstSeenMates.put(currentReadName, currentRecord) ;
        }
        else {
            assertPairedMates(firstRecord, currentRecord);


            final SAMReadGroupRecord readGroup = currentRecord.getReadGroup();
            List<FastqWriter> writerPair;
            writerPair = writers.get(readGroup);
            if(writerPair == null)
            {
                final File fq1 = makeReadGroupFile(readGroup, "_1");

View Full Code Here

Examples of net.sf.samtools.SAMReadGroupRecord

            }
        }
    }


    protected void doGroupedUnpaired(final Map<SAMReadGroupRecord, List<FastqWriter>> writers, final SAMRecord currentRecord) {
        final SAMReadGroupRecord readGroup = currentRecord.getReadGroup();
        final SAMFileReader reader = new SAMFileReader(IoUtil.openFileForReading(INPUT));


        List<FastqWriter> writerList = writers.get(readGroup);
        if(writerList == null){
            final File fq1 = makeReadGroupFile(readGroup, null);

View Full Code Here

0 1 2 3

TOP

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.