Package htsjdk.samtools

Examples of htsjdk.samtools.SAMFileReader.queryOverlapping()

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        SAMFileReader writtenReader = new SAMFileReader(new File(outPath));
        writtenReader.setValidationStringency(ValidationStringency.SILENT);
        SAMRecordIterator iter = null;
        if(createIndex){
            iter = writtenReader.queryOverlapping(sequence, start + 1, end);
        }else{
            iter = writtenReader.iterator();
        }

        int readCount = 0;
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        reader = new SAMFileReader(bamFile);
        reader.setValidationStringency(ValidationStringency.SILENT);
        reader.enableIndexCaching(true);
        index = reader.getIndex();

        reader.queryOverlapping(contigName,1,reader.getFileHeader().getSequence(contigName).getSequenceLength()).close();

        int numBins = 0;
        int numChunks = 0;
        int numLinearIndexEntries = 0;
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