Examples with SynchronousReferenceLookupAdapter au.edu.wehi.idsv.picard.SynchronousReferenceLookupAdapter used on opensource projects

Example 6 with SynchronousReferenceLookupAdapter

use of au.edu.wehi.idsv.picard.SynchronousReferenceLookupAdapter in project gridss by PapenfussLab.

the class Manual method assembly_scoring_should_be_symmetrical.

// @Test
@Category(Hg19Tests.class)
public void assembly_scoring_should_be_symmetrical() throws FileNotFoundException {
    File sam = new File("W:/debug/test.bam");
    File ref = Hg19Tests.findHg19Reference();
    ProcessingContext pc = new ProcessingContext(getFSContext(), ref, new SynchronousReferenceLookupAdapter(new IndexedFastaSequenceFile(ref)), null, getConfig());
    SAMEvidenceSource ses = new SAMEvidenceSource(pc, sam, null, 0);
    List<SAMRecord> reads = getRecords(new File("W:/debug/test.bam.gridss.working/test.bam.sv.bam"));
    List<SplitReadEvidence> list = ses.iterator().stream().filter(e -> e instanceof SplitReadEvidence).map(e -> (SplitReadEvidence) e).filter(e -> e.getSAMRecord().getReadName().equals("variant.chr12-art1000553")).collect(Collectors.toList());
    for (SplitReadEvidence e : list) {
        e.getBreakpointQual();
    }
}

Example 7 with SynchronousReferenceLookupAdapter

use of au.edu.wehi.idsv.picard.SynchronousReferenceLookupAdapter in project gridss by PapenfussLab.

the class ExtractSVReadsTest method regression_should_extract_split_read_alignments_as_group.

// @Test
@Category(Hg38Tests.class)
public void regression_should_extract_split_read_alignments_as_group() throws IOException {
    File ref = Hg38Tests.findHg38Reference();
    ReferenceLookup lookup = new SynchronousReferenceLookupAdapter(new IndexedFastaSequenceFile(ref));
    Files.copy(new File("src/test/resources/sa.split/test1.sam"), input);
    ExtractSVReads extract = new ExtractSVReads();
    // new ProcessingContext(getFSContext(), ref, lookup, null, getConfig());
    extract.setReference(lookup);
    extract.MIN_CLIP_LENGTH = 4;
    extract.INSERT_SIZE_METRICS = new File("src/test/resources/sa.split/test.insert_size_metrics");
    extract.READ_PAIR_CONCORDANCE_METHOD = ReadPairConcordanceMethod.PERCENTAGE;
    extract.OUTPUT = output;
    extract.INPUT = input;
    try (SamReader reader = SamReaderFactory.make().open(input)) {
        extract.setup(reader.getFileHeader(), input);
    }
    List<SAMRecord> records = getRecords(input);
    List<Boolean> result = records.stream().map(r -> extract.shouldExtract(ImmutableList.of(r), lookup)[0]).collect(Collectors.toList());
    /*
		for (int i = 0; i < records.size(); i++) {
			SAMRecord r = records.get(i);
			System.out.print(r.getSupplementaryAlignmentFlag() ? "S" : " ");
			System.out.print(r.getFirstOfPairFlag() ? "1" : "2");
			System.out.print(" Extracted=" + (result.get(i) ? "y" : "n"));
			System.out.print(" HasConcPair=" + (ExtractSVReads.hasReadPairingConsistentWithReference(extract.getReadPairConcordanceCalculator(), ImmutableList.of(r)) ? "y" : "n"));
			boolean[] ra = ExtractSVReads.hasReadAlignmentConsistentWithReference(ImmutableList.of(r));
			System.out.print(" HasConcRead=" + (ra[0] ? "y" : "n") + (ra[1] ? "y" : "n"));
			System.out.println(" " + new ChimericAlignment(r).toString());
		}
		*/
    Assert.assertEquals(records.stream().map(r -> r.getSecondOfPairFlag()).collect(Collectors.toList()), result);
    lookup.close();
}