| /dports/biology/freebayes/freebayes-1.3.5/python/ |
| H A D | allelebayes.py | 61 def group_alleles(alleles): argument
71 def alleles_quality_to_lnprob(alleles): argument
131 def sampling_prob(genotype, alleles): argument
188 def data_likelihood_estimate(genotype, alleles): argument
250 def genotype_probabilities(genotypes, alleles): argument
253 def genotype_probabilities_heuristic(genotypes, alleles): argument
304 … alleles = [allele for allele in sample['alleles'] if allele['type'] in ['reference', 'snp']] variable
305 alleles = alleles_quality_to_lnprob(alleles) variable
315 alleles = sample['alleles'] variable
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/ |
| H A D | AlleleSpecificAnnotationDataUnitTest.java | 19 final List<Allele> alleles= Arrays.asList(Aref, T); in testCreate() local
22 Assert.assertEquals(asad.getAlleles(), alleles); in testCreate() local
40 final List<Allele> alleles= Arrays.asList(A, T); in testNoRef() local
49 final List<Allele> alleles= Arrays.asList(Aref, Tref); in testTwoRef() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/genotyper/ |
| H A D | IndexedAlleleList.java | 16 private final IndexedSet<A> alleles; field in IndexedAlleleList
40 public IndexedAlleleList(final A... alleles) { in IndexedAlleleList()
56 public IndexedAlleleList(final Collection<A> alleles) { in IndexedAlleleList()
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| H A D | AlleleLikelihoods.java | 81 protected AlleleList<A> alleles; field in AlleleLikelihoods
121 final AlleleList<A> alleles, in AlleleLikelihoods()
150 AlleleLikelihoods(final AlleleList alleles, in AlleleLikelihoods()
191 private static int findReferenceAllele(final AlleleList<?> alleles) { in findReferenceAllele()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/genotyper/ |
| H A D | AlleleLikelihoodsUnitTest.java | 30 …public void testInstantiationAndQuery(final String[] samples, final Allele[] alleles, final Map<St… in testInstantiationAndQuery()
44 …public void testLikelihoodFillingAndQuery(final String[] samples, final Allele[] alleles, final Ma… in testLikelihoodFillingAndQuery()
50 …private double[][][] fillWithRandomLikelihoods(final String[] samples, final Allele[] alleles, fin… in fillWithRandomLikelihoods()
65 …private double[][][] fillWithRandomLikelihoods(final String[] samples, final Allele[] alleles, fin… in fillWithRandomLikelihoods()
73 …public void testBestAlleles(final String[] samples, final Allele[] alleles, final Map<String,List<… in testBestAlleles()
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| H A D | IndexedAlleleListUnitTest.java | 29 … final Allele[] alleles = AlleleListUnitTester.generateRandomAlleles(alleleCount, maxAlleleLength); in testArrayConstructor() local
38 … final Allele[] alleles = AlleleListUnitTester.generateRandomAlleles(alleleCount, maxAlleleLength); in testCollectionConstructor() local
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| /dports/biology/freebayes/freebayes-1.3.5/src/ |
| H A D | Allele.cpp | 133 void updateAllelesCachedData(vector<Allele*>& alleles) { in updateAllelesCachedData()
328 string stringForAlleles(vector<Allele> &alleles) { in stringForAlleles()
336 string tojson(vector<Allele*> &alleles) { in tojson()
398 ostream &operator<<(ostream &out, list<Allele*> &alleles) { in operator <<()
499 bool areHomozygous(vector<Allele*>& alleles) { in areHomozygous()
510 map<Allele, int> countAlleles(vector<Allele*>& alleles) { in countAlleles()
556 map<Allele, int> countAlleles(vector<Allele>& alleles) { in countAlleles()
570 map<Allele, int> countAlleles(list<Allele*>& alleles) { in countAlleles()
594 vector<Allele> uniqueAlleles(list<Allele*>& alleles) { in uniqueAlleles()
645 vector<Allele*>& alleles = g->second; in homogenizeAlleles() local
[all …]
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| H A D | Sample.cpp | 68 vector<Allele*>& alleles = g->second; in qualSum() local
84 vector<Allele*>& alleles = g->second; in partialQualSum() local
194 vector<Allele*>& alleles = g->second; in sortReferenceAlleles() local
202 vector<Allele*> alleles; in sortReferenceAlleles() local
222 vector<Allele*>& alleles = s->second; in strandBaseCount() local
248 vector<Allele*>& alleles = g->second; in baseCount() local
264 vector<Allele*>& alleles = g->second; in tojson() local
279 const vector<Allele*>& alleles = g->second; in groupAlleles() local
302 vector<Allele*>& alleles = group->second; in sufficientAlternateObservations() local
355 void Samples::assignPartialSupport(vector<Allele>& alleles, in assignPartialSupport()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/afcalc/ |
| H A D | AlleleFrequencyCalculatorUnitTest.java | 45 final List<Allele> alleles = Arrays.asList(A,B,C); in testSymmetries() local
78 final List<Allele> alleles = Arrays.asList(A,B,C); in testMLECounts() local
114 final List<Allele> alleles = Arrays.asList(A,B); in testManySamplesWithLowConfidence() local
140 final List<Allele> alleles = Arrays.asList(A,B,C); in testManyVeryConfidentSamples() local
170 final List<Allele> alleles = Arrays.asList(A,B); in testApproximateMultiplicativeConfidence() local
197 final List<Allele> alleles = Arrays.asList(A,B); in testManyRefSamplesDontKillGoodVariant() local
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| H A D | AFCalculationResultUnitTest.java | 31 …private void test(final int[] mleCounts, final List<Allele> alleles, final double probabilityOfNoV… in test()
39 Assert.assertEquals(result.getAllelesUsedInGenotyping(), alleles); in test() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/ |
| H A D | SubsettedLikelihoodMatrix.java | 24 private final List<A> alleles; field in SubsettedLikelihoodMatrix
27 …blic SubsettedLikelihoodMatrix(final LikelihoodMatrix<EVIDENCE, A> matrix, final List<A> alleles) { in SubsettedLikelihoodMatrix()
37 …final List<A> alleles = matrix.alleles().stream().filter(a -> !basesMatch(a,excludedAllele)).colle… in excludingAllele() local
49 public List<A> alleles() { return alleles; } in alleles() method in SubsettedLikelihoodMatrix
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ |
| H A D | LocationAndAlleles.java | 14 private final List<Allele> alleles; field in LocationAndAlleles
16 public LocationAndAlleles(final int loc, final List<Allele> alleles) { in LocationAndAlleles()
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| /dports/biology/haplohseq/haplohseq-0.1.2/src/test/ |
| H A D | InputProcessorTest.cpp | 23 std::vector< std::vector<char> > alleles; in BOOST_AUTO_TEST_CASE() local
54 std::vector< std::vector<char> > alleles; in BOOST_AUTO_TEST_CASE() local
91 std::vector< std::vector<char> > alleles; in BOOST_AUTO_TEST_CASE() local
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| H A D | HaplohSeqTest.cpp | 20 std::vector< std::vector<char> > alleles; in BOOST_AUTO_TEST_CASE() local
37 std::vector< std::vector<char> > alleles; in BOOST_AUTO_TEST_CASE() local
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| /dports/biology/lamarc/lamarc-2.1.8/src/datalike/ |
| H A D | phenotypes.cpp | 50 void Phenotypes::AddPhenotype(const StringVec1d& alleles, string name, double penetrance) in AddPhenotype()
68 Haplotypes Phenotypes::ChooseHaplotypes(const StringVec1d& alleles) in ChooseHaplotypes()
176 multiset<string> alleles = (*genotype).first; in MakeHaplotypes() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ |
| H A D | DepthPerAlleleBySample.java | 54 final Set<Allele> alleles = new LinkedHashSet<>(vc.getAlleles()); in annotate() local
62 …protected int[] annotateWithLikelihoods(VariantContext vc, Genotype g, Set<Allele> alleles, final … in annotateWithLikelihoods()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/ |
| H A D | GenotypingEngine.java | 201 …protected double phredNoVariantPosteriorProbability(final List<Allele> alleles, final GenotypesCon… in phredNoVariantPosteriorProbability()
208 private double extractPNoAlt(final List<Allele> alleles, final Genotype gt) { in extractPNoAlt()
215 …private double extractPNoAlt(final List<Allele> alleles, final Genotype gt, final double[] posteri… in extractPNoAlt()
261 private final List<Allele> alleles; field in GenotypingEngine.OutputAlleleSubset
265 …private OutputAlleleSubset(final List<Allele> alleles, final List<Integer> mleCounts, final boolea… in OutputAlleleSubset()
293 final List<Allele> alleles = afCalculationResult.getAllelesUsedInGenotyping(); in calculateOutputAlleleSubset() local
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| H A D | GenotypingLikelihoods.java | 20 private final AlleleList<A> alleles; field in GenotypingLikelihoods
37 …GenotypingLikelihoods(final AlleleList<A> alleles, final PloidyModel ploidyModel, final List<Genot… in GenotypingLikelihoods()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ |
| H A D | LeftAlignAndTrimVariantsUnitTest.java | 70 final List<Allele> alleles = new ArrayList<Allele>(); in LeftAlignTestData() local
114 final List<Allele> alleles = new ArrayList<Allele>(); in LeftAlignTestData() local
150 … final List<Allele> alleles = Arrays.asList(Allele.create("AA", true), Allele.create("A", false)); in testLeftAlignWithVaryingMaxDistances() local
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| /dports/biology/vt/vt-0.57721/ |
| H A D | variant_manip.cpp | 111 char** alleles = bcf_get_allele(v); in is_normalized() local
204 char** alleles = bcf_get_allele(v); in contains_N() local
513 void VariantManip::right_trim_or_left_extend(std::vector<std::string>& alleles, int32_t& pos1, cons… in right_trim_or_left_extend()
588 void VariantManip::left_trim(std::vector<std::string>& alleles, int32_t& pos1, int32_t& left_trimme… in left_trim()
623 std::vector<std::string>& alleles, //store alleles in generate_probes()
740 std::vector<std::string>& alleles, in generate_probes()
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| /dports/biology/jalview/jalview/test/jalview/ext/htsjdk/ |
| H A D | VCFReaderTest.java | 51 List<Allele> alleles = vc.getAlleles(); in testReadVcf_plain() local
188 List<Allele> alleles = vc.getAlleles(); in testQuery_plain() local
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| /dports/biology/vcflib/vcflib-1.0.2/src/ |
| H A D | vcfroc.cpp | 274 vector<VariantAllele>& alleles = parsedAlleles[&*v][**a]; in main() local
302 vector<VariantAllele>& alleles = parsedAlleles[*v][**a]; in main() local
311 vector<VariantAllele>& alleles = parsedAlts[**a]; in main() local
350 vector<VariantAllele*>& alleles = a->second; in main() local
412 vector<VariantAllele*>& alleles = a->second; in main() local
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/ |
| H A D | vcfroc.cpp | 264 vector<VariantAllele>& alleles = parsedAlleles[&*v][**a]; in main() local
292 vector<VariantAllele>& alleles = parsedAlleles[*v][**a]; in main() local
301 vector<VariantAllele>& alleles = parsedAlts[**a]; in main() local
340 vector<VariantAllele*>& alleles = a->second; in main() local
402 vector<VariantAllele*>& alleles = a->second; in main() local
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib/src/ |
| H A D | vcfroc.cpp | 264 vector<VariantAllele>& alleles = parsedAlleles[&*v][**a]; in main() local
292 vector<VariantAllele>& alleles = parsedAlleles[*v][**a]; in main() local
301 vector<VariantAllele>& alleles = parsedAlts[**a]; in main() local
340 vector<VariantAllele*>& alleles = a->second; in main() local
402 vector<VariantAllele*>& alleles = a->second; in main() local
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| /dports/biology/bamutil/bamUtil-1.0.15/libStatGen/general/ |
| H A D | GenotypeLists.h | 28 IntArray alleles; variable
|