Examples with BAMIndexer htsjdk.samtools.BAMIndexer used on opensource projects

Example 1 with BAMIndexer

use of htsjdk.samtools.BAMIndexer in project gatk by broadinstitute.

the class CreateHadoopBamSplittingIndex method createBaiAndSplittingIndex.

private static void createBaiAndSplittingIndex(final File inputBam, final File index, final int granularity, final ValidationStringency readValidationStringency) {
    assertIsBam(inputBam);
    try (SamReader reader = SamReaderFactory.makeDefault().validationStringency(readValidationStringency).setOption(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS, true).open(inputBam);
        BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(index))) {
        final SAMFileHeader header = reader.getFileHeader();
        assertBamIsCoordinateSorted(header);
        final SplittingBAMIndexer indexer = new SplittingBAMIndexer(out, granularity);
        final BAMIndexer bamIndexer = new BAMIndexer(IOUtils.replaceExtension(index, BAMIndex.BAMIndexSuffix), header);
        for (final SAMRecord read : reader) {
            indexer.processAlignment(read);
            bamIndexer.processAlignment(read);
        }
        indexer.finish(inputBam.length());
        bamIndexer.finish();
    } catch (final IOException e) {
        throw new UserException("Couldn't create splitting index", e);
    }
}