Examples of net.sf.samtools.SAMReadGroupRecord

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);
    }
  }

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    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)

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      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;
  }

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            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");

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            }
        }
    }


    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);

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Related Classes of net.sf.samtools.SAMReadGroupRecord

edu.wustl.genome.samtools.GCSamToFastq

net.sf.cram.Cram2BamRecordFactory

net.sf.cram.Sam2CramRecordFactory

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