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Searched defs:ploidy (Results 1 – 25 of 120) sorted by relevance

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/dports/biology/bcftools/bcftools-1.14/
H A Dploidy.c45 int sex, ploidy; member
50 regidx_t *ploidy_regions(ploidy_t *ploidy) in ploidy_regions()
58 ploidy_t *ploidy = (ploidy_t*) usr; in ploidy_parse() local
122 static void _set_defaults(ploidy_t *ploidy, int dflt) in _set_defaults()
181 void ploidy_destroy(ploidy_t *ploidy) in ploidy_destroy()
229 int ploidy_nsex(ploidy_t *ploidy) in ploidy_nsex()
234 char *ploidy_id2sex(ploidy_t *ploidy, int id) in ploidy_id2sex()
240 int ploidy_sex2id(ploidy_t *ploidy, char *sex) in ploidy_sex2id()
247 int ploidy_add_sex(ploidy_t *ploidy, const char *sex) in ploidy_add_sex()
259 int ploidy_max(ploidy_t *ploidy) in ploidy_max()
[all …]
/dports/biology/bio-mocha/bcftools-1.14/
H A Dploidy.c45 int sex, ploidy; member
50 regidx_t *ploidy_regions(ploidy_t *ploidy) in ploidy_regions()
58 ploidy_t *ploidy = (ploidy_t*) usr; in ploidy_parse() local
122 static void _set_defaults(ploidy_t *ploidy, int dflt) in _set_defaults()
181 void ploidy_destroy(ploidy_t *ploidy) in ploidy_destroy()
229 int ploidy_nsex(ploidy_t *ploidy) in ploidy_nsex()
234 char *ploidy_id2sex(ploidy_t *ploidy, int id) in ploidy_id2sex()
240 int ploidy_sex2id(ploidy_t *ploidy, char *sex) in ploidy_sex2id()
247 int ploidy_add_sex(ploidy_t *ploidy, const char *sex) in ploidy_add_sex()
259 int ploidy_max(ploidy_t *ploidy) in ploidy_max()
[all …]
/dports/biology/py-pysam/pysam-0.18.0/bcftools/
H A Dploidy.c45 int sex, ploidy; member
50 regidx_t *ploidy_regions(ploidy_t *ploidy) in ploidy_regions()
58 ploidy_t *ploidy = (ploidy_t*) usr; in ploidy_parse() local
122 static void _set_defaults(ploidy_t *ploidy, int dflt) in _set_defaults()
181 void ploidy_destroy(ploidy_t *ploidy) in ploidy_destroy()
229 int ploidy_nsex(ploidy_t *ploidy) in ploidy_nsex()
234 char *ploidy_id2sex(ploidy_t *ploidy, int id) in ploidy_id2sex()
240 int ploidy_sex2id(ploidy_t *ploidy, char *sex) in ploidy_sex2id()
247 int ploidy_add_sex(ploidy_t *ploidy, const char *sex) in ploidy_add_sex()
259 int ploidy_max(ploidy_t *ploidy) in ploidy_max()
[all …]
H A Dploidy.c.pysam.c47 int sex, ploidy; member
52 regidx_t *ploidy_regions(ploidy_t *ploidy) in ploidy_regions()
60 ploidy_t *ploidy = (ploidy_t*) usr; in ploidy_parse() local
124 static void _set_defaults(ploidy_t *ploidy, int dflt) in _set_defaults()
183 void ploidy_destroy(ploidy_t *ploidy) in ploidy_destroy()
231 int ploidy_nsex(ploidy_t *ploidy) in ploidy_nsex()
236 char *ploidy_id2sex(ploidy_t *ploidy, int id) in ploidy_id2sex()
242 int ploidy_sex2id(ploidy_t *ploidy, char *sex) in ploidy_sex2id()
249 int ploidy_add_sex(ploidy_t *ploidy, const char *sex) in ploidy_add_sex()
261 int ploidy_max(ploidy_t *ploidy) in ploidy_max()
[all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/
H A DGenotypeLikelihoodCalculatorsUnitTest.java49 …public void testGenotypeCountSharedInstance(int ploidy, int alleleCount, int expected) throws Exce… in testGenotypeCountSharedInstance()
54 …public void testInstanceSharedInstance(int ploidy, int alleleCount, int expected) throws Exception… in testInstanceSharedInstance()
58 Assert.assertEquals(inst.ploidy(), ploidy); in testInstanceSharedInstance() local
64 …public void testGenotypeCountNewInstance(int ploidy, int alleleCount, int expected) throws Excepti… in testGenotypeCountNewInstance()
69 … public void testInstanceNewInstance(int ploidy, int alleleCount, int expected) throws Exception { in testInstanceNewInstance()
73 Assert.assertEquals(inst.ploidy(), ploidy); in testInstanceNewInstance() local
H A DHomogeneousPloidyModelUnitTest.java24 public void testPloidyAndSampleList(final int ploidy, final int sampleCount) { in testPloidyAndSampleList()
32 Assert.assertEquals(ploidyModel.totalPloidy(), sampleCount * ploidy); in testPloidyAndSampleList() local
35 Assert.assertEquals(ploidyModel.samplePloidy(i), ploidy); in testPloidyAndSampleList() local
H A DGenotypeAlleleCountsUnitTest.java69 public void testFirst(final int ploidy) { in testFirst()
72 assertEquals(subject.ploidy(), ploidy); in testFirst() local
99 public void testNext(final int ploidy) { in testNext()
110 public void testIncrease(final int ploidy) { in testIncrease()
H A DGenotypeLikelihoodCalculatorUnitTest.java25 public void testPloidyAndMaximumAllele(final int ploidy, final int alleleCount) { in testPloidyAndMaximumAllele()
28 Assert.assertEquals(calculator.ploidy(), ploidy); in testPloidyAndMaximumAllele() local
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/
H A DGenotypeLikelihoodCalculators.java237 …private static GenotypeAlleleCounts[] buildGenotypeAlleleCountsArray(final int ploidy, final int a… in buildGenotypeAlleleCountsArray()
261 …public synchronized GenotypeLikelihoodCalculator getInstance(final int ploidy, final int alleleCou… in getInstance()
271 …private synchronized void calculateGenotypeCountsUsingTablesAndValidate(final int ploidy, final in… in calculateGenotypeCountsUsingTablesAndValidate()
290 …public synchronized GenotypeLikelihoodCalculatorDRAGEN getInstanceDRAGEN(final int ploidy, final i… in getInstanceDRAGEN()
342 private static void checkPloidyAndMaximumAllele(final int ploidy, final int maximumAllele) { in checkPloidyAndMaximumAllele()
366 public int genotypeCount(final int ploidy, final int alleleCount) { in genotypeCount()
383 public static int computeMaxAcceptableAlleleCount(final int ploidy, final int maxGenotypeCount){ in computeMaxAcceptableAlleleCount()
412 private synchronized int calculateGenotypeCountUsingTables(int ploidy, int alleleCount) { in calculateGenotypeCountUsingTables()
H A DHomogeneousPloidyModel.java14 private final int ploidy; field in HomogeneousPloidyModel
25 public HomogeneousPloidyModel(final SampleList sampleList, final int ploidy) { in HomogeneousPloidyModel()
H A DGenotypeAlleleCounts.java90 private final int ploidy; field in GenotypeAlleleCounts
132 … private GenotypeAlleleCounts(final int ploidy, final int index, final int... sortedAlleleCounts) { in GenotypeAlleleCounts()
136 …private GenotypeAlleleCounts(final int ploidy, final int index, final int[] sortedAlleleCounts, fi… in GenotypeAlleleCounts()
143 public int ploidy() { return ploidy; } in ploidy() method in GenotypeAlleleCounts
H A DAlleleSubsettingUtils.java67 final int ploidy = g.getPloidy() > 0 ? g.getPloidy() : defaultPloidy; in subsetAlleles() local
342 final int ploidy = genotype.getPloidy() > 0 ? genotype.getPloidy() : defaultPloidy; in calculateLikelihoodSums() local
369 …public static int[] subsettedPLIndices(final int ploidy, final List<Allele> originalAlleles, final… in subsettedPLIndices()
478 … private static int indexOfBestDel(final List<Allele> alleles, final int[] PLs, final int ploidy) { in indexOfBestDel()
503 …ic int findHomIndex(final GenotypeLikelihoodCalculator calculator, final int i, final int ploidy) { in findHomIndex()
/dports/biology/freebayes/freebayes-1.3.5/src/
H A DCNV.cpp11 int ploidy = atoi(fields.at(1).c_str()); in load() local
19 int ploidy = atoi(fields.at(4).c_str()); in load() local
36 void CNVMap::setSamplePloidy(const string& sample, int ploidy) { in setSamplePloidy()
40 …Map::setPloidy(string const& sample, string const& seq, long int start, long int end, int ploidy) { in setPloidy()
44 int CNVMap::ploidy(string const& sample, string const& seq, long int position) { in ploidy() function in CNVMap
/dports/biology/bcftools/bcftools-1.14/plugins/
H A Dfixploidy.c41 static ploidy_t *ploidy = NULL; variable
81 void set_samples(char *fname, bcf_hdr_t *hdr, ploidy_t *ploidy, int *sample2sex) in set_samples()
207 int ploidy = force_ploidy!=-1 ? force_ploidy : sex2ploidy[ sample2sex[i] ]; in process() local
225 int ploidy = force_ploidy!=-1 ? force_ploidy : sex2ploidy[ sample2sex[i] ]; in process() local
/dports/biology/bio-mocha/bcftools-1.14/plugins/
H A Dfixploidy.c41 static ploidy_t *ploidy = NULL; variable
81 void set_samples(char *fname, bcf_hdr_t *hdr, ploidy_t *ploidy, int *sample2sex) in set_samples()
207 int ploidy = force_ploidy!=-1 ? force_ploidy : sex2ploidy[ sample2sex[i] ]; in process() local
225 int ploidy = force_ploidy!=-1 ? force_ploidy : sex2ploidy[ sample2sex[i] ]; in process() local
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/afcalc/
H A DAlleleFrequencyCalculator.java57 final int repeats, final int ploidy, in makeCalculator()
81 …private static int[] genotypeIndicesWithOnlyRefAndSpanDel(final int ploidy, final List<Allele> all… in genotypeIndicesWithOnlyRefAndSpanDel()
146 final int ploidy = g.getPloidy() == 0 ? defaultPloidy : g.getPloidy(); in calculate() local
215 final int ploidy = log10GenotypeLikelihoods.length - 1; in calculateSingleSampleBiallelicNonRefPosterior() local
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/
H A DSomaticReferenceConfidenceModel.java58 public ReferenceConfidenceResult calcGenotypeLikelihoodsOfRefVsAny(final int ploidy, in calcGenotypeLikelihoodsOfRefVsAny()
98 …public void doIndelRefConfCalc(final int ploidy, final byte[] ref, final ReadPileup pileup, final … in doIndelRefConfCalc()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/
H A DReferenceConfidenceModel.java192 …final int ploidy = ploidyModel.samplePloidy(0); // the first sample = the only sample in reference… in calculateRefConfidence() local
234 public VariantContext makeReferenceConfidenceVariantContext(final int ploidy, in makeReferenceConfidenceVariantContext()
267 …public void doIndelRefConfCalc(final int ploidy, final byte[] ref, final ReadPileup pileup, final … in doIndelRefConfCalc()
318 GenotypeLikelihoods getIndelPLs(final int ploidy, final int nInformativeReads) { in getIndelPLs()
322 private GenotypeLikelihoods indelPLCache(final int ploidy, final int nInformativeReads) { in indelPLCache()
326 private GenotypeLikelihoods[] initializeIndelPLCache(final int ploidy) { in initializeIndelPLCache()
365 public ReferenceConfidenceResult calcGenotypeLikelihoodsOfRefVsAny(final int ploidy, in calcGenotypeLikelihoodsOfRefVsAny()
/dports/biology/vt/vt-0.57721/
H A Destimator.cpp41 void Estimator::compute_af(int32_t *gts, int32_t no_samples, int32_t ploidy, in compute_af()
179 void Estimator::compute_gl_af_hwe(int32_t *pls, int32_t no_samples, int32_t ploidy, in compute_gl_af_hwe()
360 void Estimator::compute_gl_af(int32_t *pls, int32_t nsamples, int32_t ploidy, in compute_gl_af()
527 void Estimator::compute_hwe_lrt(int32_t *pls, int32_t no_samples, int32_t ploidy, in compute_hwe_lrt()
615 void Estimator::compute_gl_fic(int32_t * pls, int32_t no_samples, int32_t ploidy, in compute_gl_fic()
737 void Estimator::compute_gl_ab(int32_t *pls, int32_t no_samples, int32_t ploidy, in compute_gl_ab()
817 void Estimator::compute_qual(int32_t *pls, int32_t no_samples, int32_t ploidy, in compute_qual()
H A Ddecompose2.cpp203 int32_t ploidy = 0; in decompose2() local
431 int32_t ploidy = bcf_ag2p(n_allele, n_genotype); in decompose2() local
457 int32_t ploidy = bcf_ag2p(n_allele, n_genotype); in decompose2() local
672 int32_t ploidy = bcf_ag2p(n_allele, n_genotype); in decompose2() local
698 int32_t ploidy = bcf_ag2p(n_allele, n_genotype); in decompose2() local
867 int32_t ploidy = n/bcf_hdr_nsamples(odr->hdr); in decompose2() local
H A Ddecompose.cpp233 int32_t ploidy = 0; in decompose() local
465 int32_t ploidy = bcf_ag2p(n_allele, n_genotype); in decompose() local
495 int32_t ploidy = bcf_ag2p(n_allele, n_genotype); in decompose() local
710 int32_t ploidy = bcf_ag2p(n_allele, n_genotype); in decompose() local
736 int32_t ploidy = bcf_ag2p(n_allele, n_genotype); in decompose() local
905 int32_t ploidy = n/bcf_hdr_nsamples(odr->hdr); in decompose() local
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/
H A DPosteriorProbabilitiesUtils.java218 final int ploidy, in calculatePosteriorProbs()
254 final int ploidy, in calculatePosteriorProbs()
272 …static double[] getDirichletPrior(final double[] knownCountsByAllele, final int ploidy, final bool… in getDirichletPrior()
/dports/biology/bbmap/bbmap/current/var2/
H A DVarFilter.java167 double totalMapqAvg, double readLengthAvg, int ploidy, ScafMap map, boolean considerNearby){ in passesFilter()
237 public String toString(double pairingRate, int ploidy){ in toString()
/dports/biology/freebayes/freebayes-1.3.5/python/
H A Dhwe.py33 def hwe_sampling_probln(genotype, genotypes, ploidy): argument
/dports/biology/bbmap/bbmap/current/gff/
H A DGffLine.java138 …otalQualityAvg, double totalMapqAvg, double readLengthAvg, double rarity, int ploidy, ScafMap map){ in GffLine()
233 double totalMapqAvg, double readLengthAvg, double rarity, int ploidy, ScafMap map){ in toText()
253 …Rate, double totalQualityAvg, double mapqAvg, double rarity, double minAlleleFraction, int ploidy, in toHeader()

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