Examples of org.broadinstitute.gatk.utils.GenomeLoc

org.broadinstitute.gatk.utils.GenomeLoc
Created by IntelliJ IDEA. User: mdepristo Date: Mar 2, 2009 Time: 8:50:11 AM Genome location representation. It is *** 1 *** based closed. Note that GenomeLocs start and stop values can be any positive or negative number, by design. Bound validation is a feature of the GenomeLocParser, and not a fundamental constraint of the GenomeLoc

    }


    @Test(dataProvider = "marginalizationDataSets")
    public void testMarginalizationWithOverlap(final String[] samples, final Allele[] alleles, final Map<String,List<GATKSAMRecord>> reads, final Map<Allele,List<Allele>> newToOldAlleleMapping) {
        final ReadLikelihoods<Allele> original = new ReadLikelihoods<>(new IndexedSampleList(samples), new IndexedAlleleList<>(alleles), reads);
        final GenomeLoc evenReadOverlap = locParser.createGenomeLoc(SAM_HEADER.getSequenceDictionary().getSequences().get(0).getSequenceName(),EVEN_READ_START ,EVEN_READ_START );
        fillWithRandomLikelihoods(samples, alleles, original);
        final ReadLikelihoods<Allele> marginalized = original.marginalize(newToOldAlleleMapping,evenReadOverlap);
        Assert.assertNotNull(marginalized);
        Assert.assertEquals(newToOldAlleleMapping.size(),marginalized.alleleCount());
        for (int a = 0; a < marginalized.alleleCount(); a++) {

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    public VariantContext map(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) {
        if ( tracker == null ) // RodWalkers can make funky map calls
            return null;


        final GenomeLoc loc = ref.getLocus();
        final VariantContext combinedVC = ReferenceConfidenceVariantContextMerger.merge(tracker.getPrioritizedValue(variants, loc), loc, INCLUDE_NON_VARIANTS ? ref.getBase() : null, true);
        if ( combinedVC == null )
            return null;
        return regenotypeVC(tracker, ref, combinedVC);
    }

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        return sum.combine(value);
    }


    public void onTraversalDone(List<Pair<GenomeLoc, Metrics>> results) {
        for (Pair<GenomeLoc, Metrics> r : results) {
            final GenomeLoc interval = r.getFirst();
            final Metrics metrics = r.getSecond();
            final List<GenomeLoc> overlappingIntervals = targets.getOverlapping(interval);


            simpleReport.addRow(
                    interval.toString(),
                    metrics.gccontent(),
                    metrics.baseQual(),
                    metrics.mapQual(),
                    metrics.depth(),
                    getPositionInTarget(interval, overlappingIntervals),
                    getTargetSize(overlappingIntervals),
                    baits.overlaps(interval),
                    interval.size(),
                    interpret(metrics, interval)
            );
        }
        simpleReport.print(out);
        out.close();

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        out.close();
    }


    protected static int getPositionInTarget(final GenomeLoc interval, final List<GenomeLoc> targets) {
        if (targets.size() > 0) {
            final GenomeLoc target = targets.get(0);


            // interval is larger on both ends than the target -- return the maximum distance to either side as a negative number. (min of 2 negative numbers)
            if (interval.getStart() < target.getStart() && interval.getStop() > target.getStop())
                return Math.min(target.getStart() - interval.getStart(), target.getStop() - interval.getStop());


            // interval is a left overlap -- return a negative number representing the distance between the two starts
            else if (interval.getStart() < target.getStart())
                return interval.getStart() - target.getStart();


            // interval is a right overlap -- return a negative number representing the distance between the two stops
            else if (interval.getStop() > target.getStop())
                return target.getStop() - interval.getStop();


            // interval is fully contained -- return the smallest distance to the edge of the target (left or right) as a positive number
            return Math.min(interval.getStart() - target.getStart(), target.getStop() - interval.getStop());
        }
        // if there is no overlapping interval, return int min value.
        return Integer.MIN_VALUE;
    }

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        // return null if we didn't find any usable reads/rods associated with the event
        if ( furthestStopPos == -1 )
            return null;


        GenomeLoc eventLoc = context.getLocation();
        if ( hasInsertion )
            eventLoc =  getToolkit().getGenomeLocParser().createGenomeLoc(eventLoc.getContig(), eventLoc.getStart(), eventLoc.getStart()+1);


        EVENT_TYPE eventType = (hasIndel ? (hasPointEvent ? EVENT_TYPE.BOTH : EVENT_TYPE.INDEL_EVENT) : EVENT_TYPE.POINT_EVENT);


        return new Event(eventLoc, furthestStopPos, eventType);
    }

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        Genotype sam_1_1_truth = GenotypeBuilder.create("test1_sample1", Arrays.asList(reference_A,reference_A));
        Genotype sam_1_2_truth = GenotypeBuilder.create("test1_sample2", Arrays.asList(reference_A,reference_A));
        Genotype sam_1_3_truth = GenotypeBuilder.create("test1_sample3", Arrays.asList(alt_C,alt_C));


        GenomeLoc loc = genomeLocParser.createGenomeLoc("chr1", 3, 3);
        VariantContextBuilder eval_1_builder = new VariantContextBuilder();
        VariantContextBuilder truth_1_builder = new VariantContextBuilder();


        eval_1_builder.alleles(Arrays.asList(reference_A,alt_C));
        truth_1_builder.alleles(Arrays.asList(reference_A,alt_C));
        eval_1_builder.genotypes(Arrays.asList(sam_1_1_eval,sam_1_2_eval,sam_1_3_eval));
        truth_1_builder.genotypes(Arrays.asList(sam_1_1_truth,sam_1_2_truth,sam_1_3_truth));


        eval_1_builder.loc(loc.getContig(),loc.getStart(),loc.getStop());
        truth_1_builder.loc(loc.getContig(),loc.getStart(),loc.getStop());


        Pair<VariantContext,VariantContext> testData = new Pair<VariantContext, VariantContext>(eval_1_builder.make(),truth_1_builder.make());


        return testData;
    }

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        Genotype sam_1_1_truth = GenotypeBuilder.create("test1_sample1", Arrays.asList(reference_A,reference_A));
        Genotype sam_1_2_truth = GenotypeBuilder.create("test1_sample2", Arrays.asList(reference_A,alt_C));
        Genotype sam_1_3_truth = GenotypeBuilder.create("test1_sample3", Arrays.asList(alt_C,alt_C));


        GenomeLoc loc = genomeLocParser.createGenomeLoc("chr1", 3, 3);
        VariantContextBuilder eval_1_builder = new VariantContextBuilder();
        VariantContextBuilder truth_1_builder = new VariantContextBuilder();


        eval_1_builder.alleles(Arrays.asList(reference_A,alt_C,alt_T));
        truth_1_builder.alleles(Arrays.asList(reference_A,alt_C));
        eval_1_builder.genotypes(Arrays.asList(sam_1_1_eval,sam_1_2_eval,sam_1_3_eval));
        truth_1_builder.genotypes(Arrays.asList(sam_1_1_truth,sam_1_2_truth,sam_1_3_truth));


        eval_1_builder.loc(loc.getContig(),loc.getStart(),loc.getStop());
        truth_1_builder.loc(loc.getContig(),loc.getStart(),loc.getStop());


        Pair<VariantContext,VariantContext> testData = new Pair<VariantContext, VariantContext>(eval_1_builder.make(),truth_1_builder.make());


        return testData;
    }

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        Genotype sam_1_1_truth = GenotypeBuilder.create("test1_sample1", Arrays.asList(reference_ACT,alt_AC));
        Genotype sam_1_2_truth = GenotypeBuilder.create("test1_sample2", Arrays.asList(alt_A,alt_A));
        Genotype sam_1_3_truth = GenotypeBuilder.create("test1_sample3", Arrays.asList(reference_ACT,alt_A));


        GenomeLoc loc = genomeLocParser.createGenomeLoc("chr1", 3, 5);
        VariantContextBuilder eval_1_builder = new VariantContextBuilder();
        VariantContextBuilder truth_1_builder = new VariantContextBuilder();


        eval_1_builder.alleles(Arrays.asList(reference_ACT,alt_ATT,alt_A));
        truth_1_builder.alleles(Arrays.asList(reference_ACT,alt_AC,alt_A));
        eval_1_builder.genotypes(Arrays.asList(sam_1_1_eval,sam_1_2_eval,sam_1_3_eval));
        truth_1_builder.genotypes(Arrays.asList(sam_1_1_truth,sam_1_2_truth,sam_1_3_truth));


        eval_1_builder.loc(loc.getContig(),loc.getStart(),loc.getStop());
        truth_1_builder.loc(loc.getContig(),loc.getStart(),loc.getStop());


        Pair<VariantContext,VariantContext> testData = new Pair<VariantContext, VariantContext>(eval_1_builder.make(),truth_1_builder.make());


        return testData;
    }

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        Genotype sam_1_1_truth = GenotypeBuilder.create("test1_sample1", Arrays.asList(reference_A,reference_A));
        Genotype sam_1_2_truth = GenotypeBuilder.create("test1_sample2", Arrays.asList(reference_A,alt_C));
        Genotype sam_1_3_truth = GenotypeBuilder.create("test1_sample3", Arrays.asList(Allele.NO_CALL,Allele.NO_CALL));


        GenomeLoc loc = genomeLocParser.createGenomeLoc("chr1", 3, 3);
        VariantContextBuilder eval_1_builder = new VariantContextBuilder();
        VariantContextBuilder truth_1_builder = new VariantContextBuilder();


        eval_1_builder.alleles(Arrays.asList(reference_A,alt_C,alt_T));
        truth_1_builder.alleles(Arrays.asList(reference_A,alt_C));
        eval_1_builder.genotypes(Arrays.asList(sam_1_1_eval,sam_1_2_eval,sam_1_3_eval));
        truth_1_builder.genotypes(Arrays.asList(sam_1_1_truth,sam_1_2_truth,sam_1_3_truth));


        eval_1_builder.loc(loc.getContig(),loc.getStart(),loc.getStop());
        truth_1_builder.loc(loc.getContig(),loc.getStart(),loc.getStop());


        Pair<VariantContext,VariantContext> testData = new Pair<VariantContext, VariantContext>(eval_1_builder.make(),truth_1_builder.make());


        return testData;
    }

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        Genotype sam_1_1_truth = GenotypeBuilder.create("test1_sample1", Arrays.asList(reference_A,reference_A));
        Genotype sam_1_2_truth = GenotypeBuilder.create("test1_sample2", Arrays.asList(reference_A,alt_C));
        Genotype sam_1_3_truth = GenotypeBuilder.create("test1_sample3", new ArrayList<Allele>(0));


        GenomeLoc loc = genomeLocParser.createGenomeLoc("chr1", 3, 3);
        VariantContextBuilder eval_1_builder = new VariantContextBuilder();
        VariantContextBuilder truth_1_builder = new VariantContextBuilder();


        eval_1_builder.alleles(Arrays.asList(reference_A,alt_C,alt_T));
        truth_1_builder.alleles(Arrays.asList(reference_A,alt_C));
        eval_1_builder.genotypes(Arrays.asList(sam_1_1_eval,sam_1_2_eval,sam_1_3_eval));
        truth_1_builder.genotypes(Arrays.asList(sam_1_1_truth,sam_1_2_truth,sam_1_3_truth));


        eval_1_builder.loc(loc.getContig(),loc.getStart(),loc.getStop());
        truth_1_builder.loc(loc.getContig(),loc.getStart(),loc.getStop());


        Pair<VariantContext,VariantContext> testData = new Pair<VariantContext, VariantContext>(eval_1_builder.make(),truth_1_builder.make());


        return testData;
    }

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