Examples with CoverageFactory com.github.lindenb.jvarkit.samtools.CoverageFactory used on opensource projects

Example 6 with CoverageFactory

use of com.github.lindenb.jvarkit.samtools.CoverageFactory in project jvarkit by lindenb.

the class BamXtremDepth method runLoop.

private void runLoop(final List<Path> bamPaths, final SamReaderFactory srf, final SAMSequenceRecord ssr, final SAMSequenceDictionary refDict, BitSet lowList, BitSet highList) throws IOException {
    final CoverageFactory coverageFactory = new CoverageFactory().setMappingQuality(mapq);
    for (final Path bamPath : bamPaths) {
        try (SamReader samReader = srf.open(bamPath)) {
            // check indexed
            if (!samReader.hasIndex()) {
                throw new JvarkitException.BamHasIndex(bamPath.toString());
            }
            final SAMFileHeader header = samReader.getFileHeader();
            // check dictionary
            final SAMSequenceDictionary dict = SequenceDictionaryUtils.extractRequired(header);
            SequenceUtil.assertSequenceDictionariesEqual(dict, refDict);
            // get the coverage in the low and high region.
            final CoverageFactory.SimpleCoverage coverage;
            if (this.alternative_algorithm) {
                LOG.info(ssr.getContig() + " " + bamPath);
                coverage = coverageFactory.getSimpleCoverage(samReader, ssr, null);
            } else {
                final List<Locatable> regions = bitSetToLocatables(ssr, lowList);
                regions.addAll(bitSetToLocatables(ssr, highList));
                if (regions.isEmpty())
                    break;
                LOG.info(ssr.getContig() + " " + bamPath + " n-intervals:" + regions.size() + " size:" + regions.stream().mapToInt(R -> R.getLengthOnReference()).sum());
                coverage = coverageFactory.getSimpleCoverage(samReader, regions, null);
            }
            // compute the new low and hight coverage
            reduce(lowList, coverage, I -> I <= this.min_coverage);
            reduce(highList, coverage, I -> I >= this.max_coverage);
        }
        System.gc();
    }
}