Examples of SAMIterator

Examples of net.sf.samtools.SAMIterator

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        .getReferenceSequenceFile(params.reference);

    FileInputStream fis = new FileInputStream(params.cramFile);
    BufferedInputStream bis = new BufferedInputStream(fis);

    SAMIterator iterator = new SAMIterator(bis,
        referenceSequenceFile);

    CramHeader cramHeader = iterator.getCramHeader();
    iterator.close();

    ProgressLogger progress = new ProgressLogger(log, 100000,
        "Validated Read");
    SamFileValidator v = new SamFileValidator(new PrintWriter(System.out),
        1);
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Examples of net.sf.samtools.SAMIterator

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                sequence.getSequenceIndex(), query.start,
                query.end - query.start));

            bis.close();

            SAMIterator it = new SAMIterator(is, refFile);
            is.seek(entries.get(0).containerStartOffset);
            BAMQueryFilteringIterator bit = new BAMQueryFilteringIterator(
                it, query.sequence, query.start, query.end,
                BAMQueryFilteringIterator.QueryType.CONTAINED,
                reader.getFileHeader());
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