Package net.sf.cram

Examples of net.sf.cram.AlignmentSliceQuery

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    SAMFileReader r1 = new SAMFileReader(params.file1);
    SAMFileReader r2 = new SAMFileReader(params.file2);

    SAMRecordIterator it1, it2;
    if (params.location != null) {
      AlignmentSliceQuery query = new AlignmentSliceQuery(params.location);
      if (SAMRecord.NO_ALIGNMENT_REFERENCE_NAME.equals(query.sequence)) {
        it1 = r1.queryUnmapped();
        it2 = r2.queryUnmapped();
      } else {
        it1 = r1.queryContained(query.sequence, query.start, query.end);
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    SAMRecordIterator it = null;
    if (params.location == null)
      it = reader.iterator();
    else {
      AlignmentSliceQuery query = new AlignmentSliceQuery(params.location);
      it = reader.query(query.sequence, query.start, query.end, false);
    }

    it = new BoundSAMRecordIterator(it, params.skipRecords,
        params.skipRecords + params.maxRecords);
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Related Classes of net.sf.cram.AlignmentSliceQuery

  • net.sf.cram.select.Dibify
  • net.sf.cram.select.SamRecordComparision
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