Package net.sf.samtools.BAMFileReader

Examples of net.sf.samtools.BAMFileReader.QueryType

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  CloseableIterator<SAMRecord> query(String sequence, int start, int end,
      boolean contained) {
    CloseableIterator<SAMRecord> iterator = queryAlignmentStart(sequence,
        start);

    QueryType qt = QueryType.CONTAINED;
    if (!contained)
      qt = QueryType.OVERLAPPING;
    if (end == -1)
      qt = QueryType.STARTING_AT;
    return new BAMQueryFilteringIterator(iterator, sequence, start, end, qt);
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Related Classes of net.sf.samtools.BAMFileReader.QueryType

  • net.sf.samtools.CRAMFileReader
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