Package htsjdk.samtools

Examples of htsjdk.samtools.SAMFileReader.enableIndexCaching()

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        SAMFileReader reader;
        BAMIndex index;

        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;
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        boolean result;
        try {
            final SAMFileReader samReader = new SAMFileReader(INPUT);
            if (!samReader.isBinary()) VALIDATE_INDEX=false;
            if (VALIDATE_INDEX){
                samReader.enableIndexCaching(true);
            }
            samReader.enableCrcChecking(true);

            final SamFileValidator validator = new SamFileValidator(out, MAX_OPEN_TEMP_FILES);
            validator.setErrorsToIgnore(IGNORE);
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