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

Example 1 with DiskBasedBAMFileIndex

use of htsjdk.samtools.DiskBasedBAMFileIndex in project hmftools by hartwigmedical.

the class BamSlicerApplication method sliceFromURLs.

private static void sliceFromURLs(@NotNull final URL indexUrl, @NotNull final URL bamUrl, @NotNull final CommandLine cmd) throws IOException {
    final File indexFile = downloadIndex(indexUrl);
    indexFile.deleteOnExit();
    final SamReader reader = SamReaderFactory.makeDefault().open(SamInputResource.of(bamUrl).index(indexFile));
    final SAMFileWriter writer = new SAMFileWriterFactory().setCreateIndex(true).makeBAMWriter(reader.getFileHeader(), true, new File(cmd.getOptionValue(OUTPUT)));
    final BAMIndex bamIndex = new DiskBasedBAMFileIndex(indexFile, reader.getFileHeader().getSequenceDictionary(), false);
    final Optional<Pair<QueryInterval[], BAMFileSpan>> queryIntervalsAndSpan = queryIntervalsAndSpan(reader, bamIndex, cmd);
    final Optional<Chunk> unmappedChunk = getUnmappedChunk(bamIndex, HttpUtils.getHeaderField(bamUrl, "Content-Length"), cmd);
    final List<Chunk> sliceChunks = sliceChunks(queryIntervalsAndSpan, unmappedChunk);
    final SamReader cachingReader = createCachingReader(indexFile, bamUrl, cmd, sliceChunks);
    queryIntervalsAndSpan.ifPresent(pair -> {
        LOGGER.info("Slicing bam on bed regions...");
        final CloseableIterator<SAMRecord> bedIterator = getIterator(cachingReader, pair.getKey(), pair.getValue().toCoordinateArray());
        writeToSlice(writer, bedIterator);
        LOGGER.info("Done writing bed slices.");
    });
    unmappedChunk.ifPresent(chunk -> {
        LOGGER.info("Slicing unmapped reads...");
        final CloseableIterator<SAMRecord> unmappedIterator = cachingReader.queryUnmapped();
        writeToSlice(writer, unmappedIterator);
        LOGGER.info("Done writing unmapped reads.");
    });
    reader.close();
    writer.close();
    cachingReader.close();
}