Examples with GenomeRegion com.hartwig.hmftools.common.region.GenomeRegion used on opensource projects

Example 11 with GenomeRegion

use of com.hartwig.hmftools.common.region.GenomeRegion in project hmftools by hartwigmedical.

the class GCAccumulatorTest method testExcludeUnmappable.

@Test
public void testExcludeUnmappable() {
    final GenomeRegion region = GenomeRegionFactory.create(CHROMOSOME, 1001, 3000);
    final GCAccumulator victim = new GCAccumulator(region);
    final GenomeRegionSelector<GCProfile> selector = selector(profile(1001, 0.90), unmappableProfile(2001, 0.91));
    selector.select(region, victim);
    assertEquals(0.90, victim.averageGCContent(), EPSILON);
}

Example 12 with GenomeRegion

use of com.hartwig.hmftools.common.region.GenomeRegion in project hmftools by hartwigmedical.

the class GCAccumulatorTest method testExcludeOverlapAtStart.

@Test
public void testExcludeOverlapAtStart() {
    final GenomeRegion region = GenomeRegionFactory.create(CHROMOSOME, 1100, 3000);
    final GCAccumulator victim = new GCAccumulator(region);
    final GenomeRegionSelector<GCProfile> selector = selector(profile(1001, 0.90), profile(2001, 0.91));
    selector.select(region, victim);
    assertEquals(0.91, victim.averageGCContent(), EPSILON);
}

Example 13 with GenomeRegion

use of com.hartwig.hmftools.common.region.GenomeRegion in project hmftools by hartwigmedical.

the class BamSlicerApplication method getIntervalsFromBED.

@NotNull
private static QueryInterval[] getIntervalsFromBED(@NotNull final String bedPath, @NotNull final SAMFileHeader header) throws IOException {
    final Slicer bedSlicer = SlicerFactory.fromBedFile(bedPath);
    final List<QueryInterval> queryIntervals = Lists.newArrayList();
    for (final GenomeRegion region : bedSlicer.regions()) {
        queryIntervals.add(new QueryInterval(header.getSequenceIndex(region.chromosome()), (int) region.start(), (int) region.end()));
    }
    return QueryInterval.optimizeIntervals(queryIntervals.toArray(new QueryInterval[queryIntervals.size()]));
}