Examples of AlignmentContext

org.apache.fop.layoutmgr.inline.AlignmentContext
The alignment context is carried within a LayoutContext and as part of the Knuth Inline elements to facilitate proper line building. All measurements are in mpt.
org.broadinstitute.gatk.engine.contexts.AlignmentContext
Useful class for forwarding on locusContext data from this iterator Created by IntelliJ IDEA. User: mdepristo Date: Feb 22, 2009 Time: 3:01:34 PM To change this template use File | Settings | File Templates.

Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

        if ( stratifiedContexts.size() == 0 )
            return null;


        int mq0 = 0;
        for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
            final AlignmentContext context = sample.getValue();
            final ReadBackedPileup pileup = context.getBasePileup();
            for (PileupElement p : pileup ) {
                if ( p.getMappingQual() == 0 )
                    mq0++;
            }
        }

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Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

        }


        Map<String,AlignmentContext> contexts = new HashMap<String,AlignmentContext>();


        for (String sample: sampleNames) {
            AlignmentContext context = new AlignmentContext(loc, generateRBPForVariant(loc, refAllele, altAllele, altBases, numReadsPerAllele, sample, addBaseErrors, phredScaledBaseErrorRate));
            contexts.put(sample,context);


        }


        return contexts;

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Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

        final LocusIteratorByState libs = new LocusIteratorByState(reads.iterator(), LocusIteratorByState.NO_DOWNSAMPLING,
                true, genomeLocParser, SampleListUtils.asSet(samples), false);


        final List<ReadBackedPileup> pileups = new LinkedList<>();
        final int startPos = activeRegionSpan.getStart();
        AlignmentContext next = libs.advanceToLocus(startPos, true);
        for ( int curPos = startPos; curPos <= activeRegionSpan.getStop(); curPos++ ) {
            if ( next != null && next.getLocation().getStart() == curPos ) {
                pileups.add(next.getBasePileup());
                next = libs.hasNext() ? libs.next() : null;
            } else {
                // no data, so we create empty pileups
                pileups.add(new ReadBackedPileupImpl(genomeLocParser.createGenomeLoc(activeRegionSpan.getContig(), curPos)));
            }

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Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

                }
            }


            // the old UG SNP-only path through the annotations
            if ( usePileup && stratifiedContexts != null ) {
                final AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
                if ( context != null ) {
                    final ReadBackedPileup pileup = context.getBasePileup();
                    if ( pileup != null )
                        fillQualsFromPileup(vc.getAlleles(), pileup, refQuals, altQuals);
                }
            }
        }

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Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

                                            Map<String,AlignmentContext> contexts) {
        // Get reference base from VCF or Reference
        if (UAC.referenceSampleName == null)
            return null;


        AlignmentContext context = contexts.get(UAC.referenceSampleName);
        ArrayList<Allele> trueReferenceAlleles = new ArrayList<Allele>();


        VariantContext referenceSampleVC;


        if (tracker != null && context != null)
            referenceSampleVC = tracker.getFirstValue(UAC.referenceSampleRod, context.getLocation());
        else
            return null;


        if (referenceSampleVC == null) {
            trueReferenceAlleles.add(Allele.create(ref.getBase(),true));

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Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

        HashMap<String, ErrorModel> perLaneErrorModels = getPerLaneErrorModels(tracker, ref, contexts);
        if (perLaneErrorModels == null && UAC.referenceSampleName != null)
            return null;


        if (UAC.TREAT_ALL_READS_AS_SINGLE_POOL) {
            AlignmentContext mergedContext = AlignmentContextUtils.joinContexts(contexts.values());
            Map<String,AlignmentContext> newContext = new HashMap<String,AlignmentContext>();
            newContext.put(DUMMY_SAMPLE_NAME,mergedContext);
            contexts = newContext;
        }
        if (contextType == AlignmentContextUtils.ReadOrientation.COMPLETE) {

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Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

                                                                Map<String, AlignmentContext> contexts) {
        VariantContext refVC =  getTrueAlleles(tracker, ref, contexts);




        // Build error model for site based on reference sample, and keep stratified for each lane.
        AlignmentContext refContext = null;
        if (UAC.referenceSampleName != null)
            refContext = contexts.get(UAC.referenceSampleName);


        ReadBackedPileup refPileup = null;
        if (refContext != null) {
            HashMap<String, ErrorModel> perLaneErrorModels = new HashMap<String, ErrorModel>();
            refPileup = refContext.getBasePileup();


            Set<String> laneIDs = new TreeSet<String>();
            if (UAC.TREAT_ALL_READS_AS_SINGLE_POOL || UAC.IGNORE_LANE_INFO)
                laneIDs.add(DUMMY_LANE);
            else

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Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

        HashMap<String, Integer> consensusIndelStrings = new HashMap<String, Integer>();


        int insCount = 0, delCount = 0;
        // quick check of total number of indels in pileup
        for ( Map.Entry<String, AlignmentContext> sample : contexts.entrySet() ) {
            final AlignmentContext context = AlignmentContextUtils.stratify(sample.getValue(), contextType);


            final ReadBackedPileup indelPileup = context.getBasePileup();
            insCount += indelPileup.getNumberOfInsertionsAfterThisElement();
            delCount += indelPileup.getNumberOfDeletionsAfterThisElement();
        }


        if ( insCount < minIndelCountForGenotyping && delCount < minIndelCountForGenotyping )
            return Collections.emptyMap();


        for (Map.Entry<String, AlignmentContext> sample : contexts.entrySet()) {
            // todo -- warning, can be duplicating expensive partition here
            AlignmentContext context = AlignmentContextUtils.stratify(sample.getValue(), contextType);


            final ReadBackedPileup indelPileup = context.getBasePileup();


            final int nIndelReads = indelPileup.getNumberOfInsertionsAfterThisElement() + indelPileup.getNumberOfDeletionsAfterThisElement();
            final int nReadsOverall = indelPileup.getNumberOfElements();


            if ( nIndelReads == 0 || (nIndelReads / (1.0 * nReadsOverall)) < minFractionInOneSample ) {

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Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext


        // For each sample, get genotype likelihoods based on pileup
        // compute prior likelihoods on haplotypes, and initialize haplotype likelihood matrix with them.


        for (Map.Entry<String, AlignmentContext> sample : contexts.entrySet()) {
            AlignmentContext context = AlignmentContextUtils.stratify(sample.getValue(), contextType);


            if (!perReadAlleleLikelihoodMap.containsKey(sample.getKey())){
                // no likelihoods have been computed for this sample at this site
                perReadAlleleLikelihoodMap.put(sample.getKey(), new PerReadAlleleLikelihoodMap());
            }
            final ReadBackedPileup pileup = context.getBasePileup();
            if (pileup != null) {
                final GenotypeBuilder b = new GenotypeBuilder(sample.getKey());
                final double[] genotypeLikelihoods = pairModel.computeDiploidReadHaplotypeLikelihoods(pileup, haplotypeMap, ref, eventLength, perReadAlleleLikelihoodMap.get(sample.getKey()), UAC.getSampleContamination().get(sample.getKey()));
                b.PL(genotypeLikelihoods);
                b.alleles(noCall);

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Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext


        // for each sample that we haven't examined yet
        final int sampleCount = samples.sampleCount();
        for (int i = 0; i < sampleCount; i++) {
            final String sample = samples.sampleAt(i);
            final AlignmentContext context = contexts.get(sample);
            if ( ignoreCoveredSamples && context != null )
                continue;
            final int depth = context == null ? 0 : context.getBasePileup().depthOfCoverage();
            log10POfRef += estimateLog10ReferenceConfidenceForOneSample(depth, theta);
        }


        return new VariantCallContext(vc, QualityUtils.phredScaleLog10CorrectRate(log10POfRef) >= configuration.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING, false);
    }

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