Examples with SamRecordFilter htsjdk.samtools.filter.SamRecordFilter used on opensource projects

Example 16 with SamRecordFilter

use of htsjdk.samtools.filter.SamRecordFilter in project ASCIIGenome by dariober.

the class UtilsTest method canCountReadsInWindow2.

@Test
public void canCountReadsInWindow2() throws InvalidGenomicCoordsException, IOException {
    GenomicCoords gc = new GenomicCoords("chr7:5524838-5611878", 80, samSeqDict, fastaFile);
    List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>();
    assertEquals(100377, Utils.countReadsInWindow("test_data/ear045.oxBS.actb.bam", gc, filters));
    filters.add(new AlignedFilter(true));
    assertEquals(100265, Utils.countReadsInWindow("test_data/ear045.oxBS.actb.bam", gc, filters));
    filters = new ArrayList<SamRecordFilter>();
    filters.add(new AlignedFilter(true));
    filters.add(new ReadNegativeStrandFilter(false));
    assertEquals(50157, Utils.countReadsInWindow("test_data/ear045.oxBS.actb.bam", gc, filters));
    filters = new ArrayList<SamRecordFilter>();
    filters.add(new AlignedFilter(true));
    filters.add(new ReadNegativeStrandFilter(true));
    assertEquals(50108, Utils.countReadsInWindow("test_data/ear045.oxBS.actb.bam", gc, filters));
    filters = FlagToFilter.flagToFilterList(80, 1026);
    assertEquals(2729, Utils.countReadsInWindow("test_data/ear045.oxBS.actb.bam", gc, filters));
    filters = FlagToFilter.flagToFilterList(80, 1026);
    filters.add(new MappingQualityFilter(30));
    assertEquals(1592, Utils.countReadsInWindow("test_data/ear045.oxBS.actb.bam", gc, filters));
}