Examples of net.sf.samtools.SAMFileReader.queryContained()

net.sf.samtools.SAMFileReader.queryContained()

Iterate over records that are contained in the given interval. Only valid to call this if hasIndex() == true.

Only a single open iterator on a given SAMFileReader may be extant at any one time. If you want to start a second iteration, the first one must be closed first.

Note that indexed lookup is not perfectly efficient in terms of disk I/O. I.e. some SAMRecords may be read and then discarded because they do not match the interval of interest.

Note that an unmapped read will be returned by this call if it has a coordinate for the purpose of sorting that is in the query region. @param sequence Reference sequence of interest. @param start 1-based, inclusive start of interval of interest. Zero implies start of the reference sequence. @param end 1-based, inclusive end of interval of interest. Zero implies end of the reference sequence. @return Iterator over the SAMRecords contained in the interval.

  public void go() throws Exception {
    System.err.println("Starting chromosome: " + chromosome);
    SAMFileReader rdr = new SAMFileReader(new File(inputFile));
    rdr.setValidationStringency(ValidationStringency.SILENT);
    
    Iterator<SAMRecord> iter = rdr.queryContained(chromosome, 0, 0);
      
    while (iter.hasNext()) {
      SAMRecord read = (SAMRecord) iter.next();
      
      outputWriter.addAlignment(read);

      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);
        it2 = r2.queryContained(query.sequence, query.start, query.end);
      }
    } else {
      it1 = r1.iterator();
      it2 = r2.iterator();
    }

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