Examples with ChromosomeLength com.hartwig.hmftools.common.chromosome.ChromosomeLength used on opensource projects

Example 1 with ChromosomeLength

use of com.hartwig.hmftools.common.chromosome.ChromosomeLength in project hmftools by hartwigmedical.

the class CountSupplier method fromBam.

@NotNull
public Multimap<Chromosome, CobaltCount> fromBam(@NotNull final String referenceBam, @NotNull final String tumorBam) throws IOException, ExecutionException, InterruptedException {
    final File tumorFile = new File(tumorBam);
    final File referenceFile = new File(referenceBam);
    final SamReaderFactory readerFactory = SamReaderFactory.make();
    final String chromosomeLengthFileName = ChromosomeLengthFile.generateFilename(outputDirectory, tumor);
    final List<ChromosomeLength> lengths;
    try (SamReader reader = readerFactory.open(tumorFile)) {
        lengths = ChromosomeLengthFactory.create(reader.getFileHeader());
    }
    ChromosomeLengthFile.write(chromosomeLengthFileName, lengths);
    LOGGER.info("Calculating Read Count from {}", tumorFile.toString());
    final List<Future<ChromosomeReadCount>> tumorFutures = createFutures(readerFactory, tumorFile, lengths);
    LOGGER.info("Calculating Read Count from {}", referenceFile.toString());
    final List<Future<ChromosomeReadCount>> referenceFutures = createFutures(readerFactory, referenceFile, lengths);
    final Multimap<String, ReadCount> tumorCounts = fromFutures(tumorFutures);
    final Multimap<String, ReadCount> referenceCounts = fromFutures(referenceFutures);
    LOGGER.info("Read Count Complete");
    return CobaltCountFactory.merge(referenceCounts, tumorCounts);
}

Example 2 with ChromosomeLength

use of com.hartwig.hmftools.common.chromosome.ChromosomeLength in project hmftools by hartwigmedical.

the class CountSupplier method createFutures.

@NotNull
private List<Future<ChromosomeReadCount>> createFutures(final SamReaderFactory readerFactory, final File file, final List<ChromosomeLength> lengths) {
    final List<Future<ChromosomeReadCount>> futures = Lists.newArrayList();
    for (ChromosomeLength chromosome : lengths) {
        final ChromosomeReadCount callable = new ChromosomeReadCount(file, readerFactory, chromosome.chromosome(), chromosome.length(), windowSize, minMappingQuality);
        futures.add(executorService.submit(callable));
    }
    return futures;
}