List of depthOfCoverage() Examples

Examples of depthOfCoverage()

org.broadinstitute.gatk.utils.pileup.ReadBackedPileup.depthOfCoverage()
@return the number of abstract elements in this pileup (reduced reads are expanded to count all reads that they represent)
org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl.depthOfCoverage()
@return the number of abstract elements in this pileup

Examples of org.broadinstitute.gatk.utils.pileup.ReadBackedPileup.depthOfCoverage()


        Assert.assertEquals(perReadAlleleLikelihoodMap.size(),pileup.depthOfCoverage());
        Assert.assertEquals(perReadAlleleLikelihoodMap.getAlleleStratifiedReadMap().keySet().size(),3);
        Map<Allele,List<GATKSAMRecord>> halfAhalfC = perReadAlleleLikelihoodMap.getAlleleStratifiedReadMap();
        Assert.assertEquals(halfAhalfC.get(base_A).size(),pileup.depthOfCoverage()/2);
        Assert.assertEquals(halfAhalfC.get(base_C).size(),pileup.depthOfCoverage()/2);
        Assert.assertEquals(halfAhalfC.get(base_T).size(),0);


        // make sure the likelihoods are retrievable


        idx = 0;

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Examples of org.broadinstitute.gatk.utils.pileup.ReadBackedPileup.depthOfCoverage()

            }
            Assert.assertEquals(perReadAlleleLikelihoodMap.size(),1+prevSize);
            prevSize = perReadAlleleLikelihoodMap.size();
        }


        Assert.assertEquals(perReadAlleleLikelihoodMap.size(),pileup.depthOfCoverage()+10);
        Assert.assertEquals(perReadAlleleLikelihoodMap.getAlleleStratifiedReadMap().get(base_A).size(),60);
        perReadAlleleLikelihoodMap.performPerAlleleDownsampling(0.1);
        Assert.assertEquals(perReadAlleleLikelihoodMap.size(),(int) (0.9*(pileup.depthOfCoverage()+10)));


        Map<Allele,List<GATKSAMRecord>> downsampledStrat = perReadAlleleLikelihoodMap.getAlleleStratifiedReadMap();

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Examples of org.broadinstitute.gatk.utils.pileup.ReadBackedPileup.depthOfCoverage()

        }


        Assert.assertEquals(perReadAlleleLikelihoodMap.size(),pileup.depthOfCoverage()+10);
        Assert.assertEquals(perReadAlleleLikelihoodMap.getAlleleStratifiedReadMap().get(base_A).size(),60);
        perReadAlleleLikelihoodMap.performPerAlleleDownsampling(0.1);
        Assert.assertEquals(perReadAlleleLikelihoodMap.size(),(int) (0.9*(pileup.depthOfCoverage()+10)));


        Map<Allele,List<GATKSAMRecord>> downsampledStrat = perReadAlleleLikelihoodMap.getAlleleStratifiedReadMap();
        Assert.assertEquals(downsampledStrat.get(base_A).size(),(int) (pileup.depthOfCoverage()/2) - 1);
        Assert.assertEquals(downsampledStrat.get(base_C).size(),(int) (pileup.depthOfCoverage()/2));
        Assert.assertEquals(downsampledStrat.get(base_T).size(),0);

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Examples of org.broadinstitute.gatk.utils.pileup.ReadBackedPileup.depthOfCoverage()

        Assert.assertEquals(perReadAlleleLikelihoodMap.getAlleleStratifiedReadMap().get(base_A).size(),60);
        perReadAlleleLikelihoodMap.performPerAlleleDownsampling(0.1);
        Assert.assertEquals(perReadAlleleLikelihoodMap.size(),(int) (0.9*(pileup.depthOfCoverage()+10)));


        Map<Allele,List<GATKSAMRecord>> downsampledStrat = perReadAlleleLikelihoodMap.getAlleleStratifiedReadMap();
        Assert.assertEquals(downsampledStrat.get(base_A).size(),(int) (pileup.depthOfCoverage()/2) - 1);
        Assert.assertEquals(downsampledStrat.get(base_C).size(),(int) (pileup.depthOfCoverage()/2));
        Assert.assertEquals(downsampledStrat.get(base_T).size(),0);
    }


    @DataProvider(name = "PoorlyModelledReadData")

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Examples of org.broadinstitute.gatk.utils.pileup.ReadBackedPileup.depthOfCoverage()

        perReadAlleleLikelihoodMap.performPerAlleleDownsampling(0.1);
        Assert.assertEquals(perReadAlleleLikelihoodMap.size(),(int) (0.9*(pileup.depthOfCoverage()+10)));


        Map<Allele,List<GATKSAMRecord>> downsampledStrat = perReadAlleleLikelihoodMap.getAlleleStratifiedReadMap();
        Assert.assertEquals(downsampledStrat.get(base_A).size(),(int) (pileup.depthOfCoverage()/2) - 1);
        Assert.assertEquals(downsampledStrat.get(base_C).size(),(int) (pileup.depthOfCoverage()/2));
        Assert.assertEquals(downsampledStrat.get(base_T).size(),0);
    }


    @DataProvider(name = "PoorlyModelledReadData")
    public Object[][] makePoorlyModelledReadData() {

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Examples of org.broadinstitute.gatk.utils.pileup.ReadBackedPileup.depthOfCoverage()

                Double likelihood = allele == base_A ? -0.04 : -3.0;
                perReadAlleleLikelihoodMap.add(e,allele,likelihood);
            }
        }


        Assert.assertEquals(perReadAlleleLikelihoodMap.size(),pileup.depthOfCoverage());
        Assert.assertEquals(perReadAlleleLikelihoodMap.getAlleleStratifiedReadMap().keySet().size(),3);
        Map<Allele,List<GATKSAMRecord>> shouldBeAllA = perReadAlleleLikelihoodMap.getAlleleStratifiedReadMap();
        Assert.assertEquals(shouldBeAllA.get(base_A).size(),pileup.depthOfCoverage());
        Assert.assertEquals(shouldBeAllA.get(base_C).size(),0);
        Assert.assertEquals(shouldBeAllA.get(base_T).size(),0);

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Examples of org.broadinstitute.gatk.utils.pileup.ReadBackedPileup.depthOfCoverage()

        }


        Assert.assertEquals(perReadAlleleLikelihoodMap.size(),pileup.depthOfCoverage());
        Assert.assertEquals(perReadAlleleLikelihoodMap.getAlleleStratifiedReadMap().keySet().size(),3);
        Map<Allele,List<GATKSAMRecord>> shouldBeAllA = perReadAlleleLikelihoodMap.getAlleleStratifiedReadMap();
        Assert.assertEquals(shouldBeAllA.get(base_A).size(),pileup.depthOfCoverage());
        Assert.assertEquals(shouldBeAllA.get(base_C).size(),0);
        Assert.assertEquals(shouldBeAllA.get(base_T).size(),0);
    }

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Examples of org.broadinstitute.gatk.utils.pileup.ReadBackedPileup.depthOfCoverage()

                perReadAlleleLikelihoodMap.add(e,allele,likelihood);
            }
            idx++;
        }


        Assert.assertEquals(perReadAlleleLikelihoodMap.size(),pileup.depthOfCoverage());
        Assert.assertEquals(perReadAlleleLikelihoodMap.getAlleleStratifiedReadMap().keySet().size(),3);
        Map<Allele,List<GATKSAMRecord>> halfAhalfC = perReadAlleleLikelihoodMap.getAlleleStratifiedReadMap();
        Assert.assertEquals(halfAhalfC.get(base_A).size(),pileup.depthOfCoverage()/2);
        Assert.assertEquals(halfAhalfC.get(base_C).size(),pileup.depthOfCoverage()/2);
        Assert.assertEquals(halfAhalfC.get(base_T).size(),0);

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Examples of org.broadinstitute.gatk.utils.pileup.ReadBackedPileup.depthOfCoverage()

        }


        Assert.assertEquals(perReadAlleleLikelihoodMap.size(),pileup.depthOfCoverage());
        Assert.assertEquals(perReadAlleleLikelihoodMap.getAlleleStratifiedReadMap().keySet().size(),3);
        Map<Allele,List<GATKSAMRecord>> halfAhalfC = perReadAlleleLikelihoodMap.getAlleleStratifiedReadMap();
        Assert.assertEquals(halfAhalfC.get(base_A).size(),pileup.depthOfCoverage()/2);
        Assert.assertEquals(halfAhalfC.get(base_C).size(),pileup.depthOfCoverage()/2);
        Assert.assertEquals(halfAhalfC.get(base_T).size(),0);


        // make sure the likelihoods are retrievable

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Examples of org.broadinstitute.gatk.utils.pileup.ReadBackedPileup.depthOfCoverage()

        li = makeLTBS(reads,createTestReadProperties(DownsamplingMethod.NONE, true));


        Assert.assertTrue(li.hasNext());
        AlignmentContext context = li.next();
        ReadBackedPileup pileup = context.getBasePileup();
        Assert.assertEquals(pileup.depthOfCoverage(), 2, "Should see only 2 reads in pileup, even with unmapped and all I reads");


        final List<GATKSAMRecord> rawReads = li.transferReadsFromAllPreviousPileups();
        Assert.assertEquals(rawReads, reads, "Input and transferred read lists should be the same, and include the unmapped and all I reads");
    }

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