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

net.sf.samtools.SAMFileReader.query()

Iterate over records that match 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. You can use a second SAMFileReader to iterate in parallel over the same underlying file.

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. @param contained If true, each SAMRecord returned is will have its alignment completely contained in theinterval of interest. If false, the alignment of the returned SAMRecords need only overlap the interval of interest. @return Iterator over the SAMRecords matching the interval.

        SAMFileReader reader = new SAMFileReader(file, index);
        source.reader = reader;
        if (query == null)
          source.it = reader.iterator();
        else
          source.it = reader.query(query.sequence, query.start,
              query.end, true);
      } else {
        index = new File(file.getAbsolutePath() + ".crai");
        if (index.exists()) {
          SAMFileReader reader = new SAMFileReader(file);

    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);
    SAMFieldSelector s = new SAMFieldSelector(params.fields);

    scFactory.losslessQS = true;
    scFactory.preserveReadNames = true;
    SequenceBaseProvider provider = new ByteArraySequenceBaseProvider(refBytes);


    SAMFileReader reader = new SAMFileReader(bamFile);
    SAMRecordIterator iterator = reader.query(seqName, 0, 0, false);
    List<CramRecord> records = new ArrayList<CramRecord>();


    PairedTemplateAssembler a = new PairedTemplateAssembler();
    int counter = 0;
    int bases = 0;

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