Examples of org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele

Package org.broadinstitute.gatk.utils.genotyper

Examples of org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele

org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele
Stores the most likely and second most likely alleles, along with a threshold for assuming computing that a read is informative. If the difference between the most-likely allele and the next-most-likely allele is < INFORMATIVE_LIKELIHOOD_THRESHOLD then the most likely allele is set to "no call", and isInformative will return false. This constant can be overridden simply by using one of the version of these calls that accepts informative threshold as an argument. For convenience, there are functions called getAlleleIfInformative that return either the most likely allele, or NO_CALL if two or more alleles have likelihoods within INFORMATIVE_LIKELIHOOD_THRESHOLD of one another. By default empty allele maps will return NO_CALL, and allele maps with a single entry will return the corresponding key User: depristo Date: 3/24/13 Time: 1:39 PM


        final HashMap<Allele, Integer> alleleCounts = new HashMap<>();
        for ( final Allele allele : vc.getAlleles() ) { alleleCounts.put(allele, 0); }


        for ( final Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : perReadAlleleLikelihoodMap.getLikelihoodReadMap().entrySet()) {
            final MostLikelyAllele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue(), alleles);
            if (! a.isInformative() ) continue; // read is non-informative
            final GATKSAMRecord read = el.getKey();
            final int prevCount = alleleCounts.get(a.getMostLikelyAllele());
            alleleCounts.put(a.getMostLikelyAllele(), prevCount + 1);
        }


        final int[] counts = new int[alleleCounts.size()];
        counts[0] = alleleCounts.get(vc.getReference());
        for (int i = 0; i < vc.getAlternateAlleles().size(); i++)

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            // make sure that there's a meaningful relationship between the alleles in the perReadAlleleLikelihoodMap and our VariantContext
            if ( ! alleleLikelihoodMap.getAllelesSet().containsAll(alleles) )
                throw new IllegalStateException("VC alleles " + alleles + " not a strict subset of per read allele map alleles " + alleleLikelihoodMap.getAllelesSet());


            for (Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : alleleLikelihoodMap.getLikelihoodReadMap().entrySet()) {
                final MostLikelyAllele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue(), alleles);
                if ( a.isInformative() ) {
                    dp++;
                }
            }


            gb.DP(dp);

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                                            final int refLoc,
                                            final PerReadAlleleLikelihoodMap likelihoodMap,
                                            final List<Double> refQuals,
                                            final List<Double> altQuals) {
        for ( final Map.Entry<GATKSAMRecord, Map<Allele,Double>> el : likelihoodMap.getLikelihoodReadMap().entrySet() ) {
            final MostLikelyAllele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue());
            if ( ! a.isInformative() )
                continue; // read is non-informative


            final GATKSAMRecord read = el.getKey();
            if ( isUsableRead(read, refLoc) ) {
                final Double value = getElementForRead(read, refLoc, a);
                if ( value == null )
                    continue;


                if ( a.getMostLikelyAllele().isReference() )
                    refQuals.add(value);
                else if ( alleles.contains(a.getMostLikelyAllele()) )
                    altQuals.add(value);
            }
        }
    }

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        final int[][] table = new int[2][2];


        for (final PerReadAlleleLikelihoodMap maps : stratifiedPerReadAlleleLikelihoodMap.values() ) {
            final int[] myTable = new int[4];
            for (final Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : maps.getLikelihoodReadMap().entrySet()) {
                final MostLikelyAllele mostLikelyAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue());
                final GATKSAMRecord read = el.getKey();
                updateTable(myTable, mostLikelyAllele.getAlleleIfInformative(), read, ref, alt);
            }
            if ( passesMinimumThreshold(myTable, minCount) )
                copyToMainTable(myTable, table);
        }

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        final HashMap<Allele, Integer> alleleCounts = new HashMap<>();
        for ( final Allele allele : vc.getAlleles() ) { alleleCounts.put(allele, 0); }


        for ( final Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : perReadAlleleLikelihoodMap.getLikelihoodReadMap().entrySet()) {
            final MostLikelyAllele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue(), alleles);
            if (! a.isInformative() ) continue; // read is non-informative
            final int prevCount = alleleCounts.get(a.getMostLikelyAllele());
            alleleCounts.put(a.getMostLikelyAllele(), prevCount + 1);
        }


        final int[] counts = new int[alleleCounts.size()];
        counts[0] = alleleCounts.get(vc.getReference());
        for (int i = 0; i < vc.getAlternateAlleles().size(); i++)

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