Examples with ProcessingContext au.edu.wehi.idsv.ProcessingContext used on opensource projects

Example 21 with ProcessingContext

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

the class PairedEvidenceTracker method allMatched.

private boolean allMatched() {
    List<DirectedBreakpoint> list = new ArrayList<>(unpaired.values());
    list.sort(DirectedBreakpoint.ByStartEnd);
    for (DirectedBreakpoint e : list) {
        ProcessingContext context = e.getEvidenceSource().getContext();
        if (!MessageThrottler.Current.shouldSupress(log, "unpaired evidence")) {
            log.error(String.format("%s (%s, %f) unpaired", e.getEvidenceID(), e.getBreakendSummary().toString(context), e.getBreakpointQual()));
        }
    }
    return unpaired.isEmpty();
}

Example 22 with ProcessingContext

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

the class AnnotateReferenceCoverage method iterator.

@Override
public CloseableIterator<VariantContextDirectedBreakpoint> iterator(CloseableIterator<VariantContextDirectedBreakpoint> calls, ExecutorService threadpool) {
    ProcessingContext context = getContext();
    List<SAMEvidenceSource> sources = getSamEvidenceSources();
    AssemblyEvidenceSource asm = getAssemblySource();
    int windowSize = SAMEvidenceSource.maximumWindowSize(context, sources, asm);
    return new SequentialCoverageAnnotator<VariantContextDirectedBreakpoint>(context, sources, calls, 2 * windowSize + WINDOW_SIZE_SAFETY_MARGIN, threadpool);
}

Example 23 with ProcessingContext

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

the class MultipleSamFileCommandLineProgram method getContext.

public ProcessingContext getContext() {
    if (processContext == null) {
        GridssConfiguration config;
        try {
            config = new GridssConfiguration(CONFIGURATION_FILE, WORKING_DIR);
        } catch (ConfigurationException e) {
            throw new RuntimeException(e);
        }
        processContext = new ProcessingContext(getFileSystemContext(), REFERENCE_SEQUENCE, null, getDefaultHeaders(), config);
        processContext.setCommandLineProgram(this);
        processContext.setFilterDuplicates(IGNORE_DUPLICATES);
        processContext.setWorkerThreadCount(WORKER_THREADS);
        if (BLACKLIST != null) {
            try {
                processContext.setBlacklist(BLACKLIST);
            } catch (IOException e) {
                log.error(e, "Error loading BED blacklist. ", BLACKLIST);
                throw new RuntimeException(e);
            }
        }
    }
    return processContext;
}

Example 24 with ProcessingContext

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

the class PairedEvidenceTracker method isValidNext.

private boolean isValidNext(T evidence) {
    if (evidence instanceof DirectedBreakpoint) {
        DirectedBreakpoint e = (DirectedBreakpoint) evidence;
        ProcessingContext context = e.getEvidenceSource().getContext();
        String evidenceId = evidence.getEvidenceID();
        String partnerId = e.getRemoteEvidenceID();
        if (unpaired.containsKey(evidenceId)) {
            String msg = String.format("%s: encountered %s multiple times.", name, evidenceId);
            if (!MessageThrottler.Current.shouldSupress(log, "duplicate evidence")) {
                log.error(msg);
            }
            return false;
        }
        if (unpaired.containsKey(partnerId)) {
            DirectedBreakpoint partner = unpaired.remove(partnerId);
            // Breakpoints must be the same
            if (!partner.getBreakendSummary().remoteBreakpoint().equals(e.getBreakendSummary())) {
                String msg = String.format("%s: breakpoints %s and %s differ for evidence pair %s %s", name, e.getBreakendSummary().toString(context), partner.getBreakendSummary().toString(context), e.getEvidenceID(), partner.getEvidenceID());
                if (!MessageThrottler.Current.shouldSupress(log, "asymetric evidence breakpoint positions")) {
                    log.error(msg);
                }
                return false;
            }
            // Scores must be the same
            if (partner.getBreakpointQual() != e.getBreakpointQual()) {
                String msg = String.format("%s: scores %f and %f differ for evidence pair %s %s", name, e.getBreakpointQual(), partner.getBreakpointQual(), e.getEvidenceID(), partner.getEvidenceID());
                if (!MessageThrottler.Current.shouldSupress(log, "asymetric evidence backpoint quality")) {
                    log.error(msg);
                }
                return false;
            }
        } else {
            unpaired.put(evidenceId, e);
        }
    }
    return true;
}

Example 25 with ProcessingContext

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

the class AllocateEvidenceTest method should_uniquely_assign.

@Test
public void should_uniquely_assign() throws IOException, InterruptedException, ExecutionException {
    final int fragSize = 4;
    final int testSize = 64;
    final List<SAMRecord> in = new ArrayList<SAMRecord>();
    final ProcessingContext pc = getCommandlineContext();
    pc.getVariantCallingParameters().writeFiltered = true;
    pc.getVariantCallingParameters().minScore = 0;
    StubSAMEvidenceSource ses = new StubSAMEvidenceSource(pc, input, 0, 0, fragSize);
    for (int i = 1; i < testSize; i++) {
        for (int j = 1; j < testSize; j++) {
            SAMRecord[] dp = withReadName(String.format("read-%d-%d", i, j), DP(0, i, "1M", true, 1, j, "1M", false));
            ses.evidence.add(NonReferenceReadPair.create(dp[0], dp[1], ses));
            ses.evidence.add(NonReferenceReadPair.create(dp[1], dp[0], ses));
            in.add(dp[0]);
            in.add(dp[1]);
        }
    }
    StubAssemblyEvidenceSource aes = new StubAssemblyEvidenceSource(pc);
    aes.fragSize = fragSize;
    Collections.sort(ses.evidence, DirectedEvidenceOrder.ByNatural);
    createInput(in);
    VariantCaller vc = new VariantCaller(pc, ImmutableList.<SAMEvidenceSource>of(ses), aes);
    ExecutorService threadpool = Executors.newSingleThreadExecutor();
    vc.callBreakends(output, threadpool);
    threadpool.shutdown();
    AllocateEvidence cmd = new AllocateEvidence();
    cmd.INPUT_VCF = output;
    cmd.setContext(pc);
    cmd.setAssemblySource(aes);
    cmd.setSamEvidenceSources(ImmutableList.of(ses));
    cmd.OUTPUT_VCF = new File(testFolder.getRoot(), "annotated.vcf");
    cmd.ASSEMBLY = new File(testFolder.getRoot(), "assembly.bam");
    // to shut up the command-line parsing
    createBAM(cmd.ASSEMBLY, SortOrder.coordinate, Collections.emptyList());
    cmd.doWork(null);
    // List<IdsvVariantContext> annotated = getVcf(new File(testFolder.getRoot(), "out.vcf"), null);
    List<IdsvVariantContext> rawcalls = getVcf(output, null);
    List<IdsvVariantContext> calls = getVcf(cmd.OUTPUT_VCF, null);
    assertSymmetrical(rawcalls.stream().map(x -> (VariantContextDirectedBreakpoint) x).collect(Collectors.toList()));
    assertSymmetrical(calls.stream().map(x -> (VariantContextDirectedBreakpoint) x).collect(Collectors.toList()));
    // with no filtering, annotation should not change call set
    double expectedEvidence = 0;
    for (DirectedEvidence e : ses.evidence) {
        DiscordantReadPair bp = (DiscordantReadPair) e;
        expectedEvidence += bp.getBreakpointQual();
    }
    double annotatedEvidence = 0;
    for (IdsvVariantContext e : calls) {
        annotatedEvidence += e.getPhredScaledQual();
    }
    double rawEvidence = rawcalls.stream().mapToDouble(e -> e.getPhredScaledQual()).sum();
    // unique assignment must result in the evidence total being, at most, the same
    assertTrue(annotatedEvidence <= rawEvidence);
    // each piece of evidence should be assigned to a single breakpoint so totals should match
    int rpCalls = calls.stream().mapToInt(v -> ((VariantContextDirectedBreakpoint) v).getBreakpointEvidenceCount()).sum();
    assertEquals(ses.evidence.size(), rpCalls);
    // floating point truncation on VCF is severe!
    assertEquals(expectedEvidence, annotatedEvidence, 20);
}