Examples with AssemblyConfiguration au.edu.wehi.idsv.configuration.AssemblyConfiguration used on opensource projects

Example 1 with AssemblyConfiguration

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

the class AssemblyEvidenceSource method shouldFilterAssembly.

public boolean shouldFilterAssembly(SAMRecord asm) {
    AssemblyConfiguration ap = getContext().getAssemblyParameters();
    AssemblyAttributes attr = new AssemblyAttributes(asm);
    // reference assembly
    List<SingleReadEvidence> breakends = SingleReadEvidence.createEvidence(this, 0, asm);
    if (breakends.size() == 0) {
        return true;
    }
    // too long
    int breakendLength = SAMRecordUtil.getSoftClipLength(asm, attr.getAssemblyDirection());
    if (breakendLength > ap.maxExpectedBreakendLengthMultiple * getMaxConcordantFragmentSize()) {
        log.debug(String.format("Filtering %s at %s:%d due to misassembly (breakend %dbp)", asm.getReadName(), asm.getReferenceName(), asm.getAlignmentStart(), breakendLength));
        return true;
    }
    // too few reads
    if (attr.getAssemblySupportCount() < ap.minReads) {
        return true;
    }
    // unanchored assembly that not actually any longer than any of the reads that were assembled together
    if (attr.getAssemblySupportCountSoftClip() == 0 && breakendLength <= attr.getAssemblyReadPairLengthMax()) {
        // at worst, we've created a misassembly.
        return true;
    }
    return false;
}

Example 2 with AssemblyConfiguration

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

the class AssemblyEvidenceSource method throttled.

private Iterator<DirectedEvidence> throttled(Iterator<DirectedEvidence> it) {
    AssemblyConfiguration ap = getContext().getAssemblyParameters();
    DirectedEvidenceDensityThrottlingIterator dit = new DirectedEvidenceDensityThrottlingIterator(throttled, getContext().getDictionary(), getContext().getLinear(), it, Math.max(ap.downsampling.minimumDensityWindowSize, getMaxConcordantFragmentSize()), ap.downsampling.acceptDensityPortion * ap.downsampling.targetEvidenceDensity, ap.downsampling.targetEvidenceDensity);
    getContext().registerBuffer(AssemblyEvidenceSource.class.getName() + ".throttle", dit);
    return dit;
}

Example 3 with AssemblyConfiguration

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

the class PositionalAssembler method createAssembler.

private NonReferenceContigAssembler createAssembler() {
    AssemblyConfiguration ap = context.getAssemblyParameters();
    int maxKmerSupportIntervalWidth = source.getMaxConcordantFragmentSize() - source.getMinConcordantFragmentSize() + 1;
    int maxReadLength = source.getMaxReadLength();
    int k = ap.k;
    int maxEvidenceSupportIntervalWidth = maxKmerSupportIntervalWidth + maxReadLength - k + 2;
    int maxPathLength = ap.positional.maxPathLengthInBases(maxReadLength);
    int maxPathCollapseLength = ap.errorCorrection.maxPathCollapseLengthInBases(maxReadLength);
    int anchorAssemblyLength = ap.anchorLength;
    int referenceIndex = it.peek().getBreakendSummary().referenceIndex;
    int firstPosition = it.peek().getBreakendSummary().start;
    currentContig = context.getDictionary().getSequence(referenceIndex).getSequenceName();
    ReferenceIndexIterator evidenceIt = new ReferenceIndexIterator(it, referenceIndex);
    EvidenceTracker evidenceTracker = new EvidenceTracker();
    SupportNodeIterator supportIt = new SupportNodeIterator(k, evidenceIt, source.getMaxConcordantFragmentSize(), evidenceTracker, ap.includePairAnchors, ap.pairAnchorMismatchIgnoreEndBases);
    AggregateNodeIterator agIt = new AggregateNodeIterator(supportIt);
    Iterator<KmerNode> knIt = agIt;
    if (Defaults.SANITY_CHECK_DE_BRUIJN) {
        knIt = evidenceTracker.new AggregateNodeAssertionInterceptor(knIt);
    }
    PathNodeIterator pathNodeIt = new PathNodeIterator(knIt, maxPathLength, k);
    Iterator<KmerPathNode> pnIt = pathNodeIt;
    if (Defaults.SANITY_CHECK_DE_BRUIJN) {
        pnIt = evidenceTracker.new PathNodeAssertionInterceptor(pnIt, "PathNodeIterator");
    }
    CollapseIterator collapseIt = null;
    PathSimplificationIterator simplifyIt = null;
    if (ap.errorCorrection.maxBaseMismatchForCollapse > 0) {
        if (!ap.errorCorrection.collapseBubblesOnly) {
            log.warn("Collapsing all paths is an exponential time operation. Gridss is likely to hang if your genome contains repetative sequence");
            collapseIt = new PathCollapseIterator(pnIt, k, maxPathCollapseLength, ap.errorCorrection.maxBaseMismatchForCollapse, false, 0);
        } else {
            collapseIt = new LeafBubbleCollapseIterator(pnIt, k, maxPathCollapseLength, ap.errorCorrection.maxBaseMismatchForCollapse);
        }
        pnIt = collapseIt;
        if (Defaults.SANITY_CHECK_DE_BRUIJN) {
            pnIt = evidenceTracker.new PathNodeAssertionInterceptor(pnIt, "PathCollapseIterator");
        }
        simplifyIt = new PathSimplificationIterator(pnIt, maxPathLength, maxKmerSupportIntervalWidth);
        pnIt = simplifyIt;
        if (Defaults.SANITY_CHECK_DE_BRUIJN) {
            pnIt = evidenceTracker.new PathNodeAssertionInterceptor(pnIt, "PathSimplificationIterator");
        }
    }
    currentAssembler = new NonReferenceContigAssembler(pnIt, referenceIndex, maxEvidenceSupportIntervalWidth, anchorAssemblyLength, k, source, assemblyNameGenerator, evidenceTracker, currentContig);
    VisualisationConfiguration vis = context.getConfig().getVisualisation();
    if (vis.assemblyProgress) {
        String filename = String.format("positional-%s_%d-%s.csv", context.getDictionary().getSequence(referenceIndex).getSequenceName(), firstPosition, direction);
        File file = new File(vis.directory, filename);
        PositionalDeBruijnGraphTracker exportTracker;
        try {
            exportTracker = new PositionalDeBruijnGraphTracker(file, supportIt, agIt, pathNodeIt, collapseIt, simplifyIt, evidenceTracker, currentAssembler);
            exportTracker.writeHeader();
            currentAssembler.setExportTracker(exportTracker);
        } catch (IOException e) {
            log.debug(e);
        }
    }
    currentAssembler.setTelemetry(getTelemetry());
    return currentAssembler;
}