/dports/biology/bcftools/bcftools-1.14/ |
H A D | ploidy.c | 45 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 …]
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/dports/biology/bio-mocha/bcftools-1.14/ |
H A D | ploidy.c | 45 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 …]
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/dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
H A D | ploidy.c | 45 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 …]
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H A D | ploidy.c.pysam.c | 47 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 …]
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/ |
H A D | GenotypeLikelihoodCalculatorsUnitTest.java | 49 …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
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H A D | HomogeneousPloidyModelUnitTest.java | 24 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
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H A D | GenotypeAlleleCountsUnitTest.java | 69 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()
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H A D | GenotypeLikelihoodCalculatorUnitTest.java | 25 public void testPloidyAndMaximumAllele(final int ploidy, final int alleleCount) { in testPloidyAndMaximumAllele() 28 Assert.assertEquals(calculator.ploidy(), ploidy); in testPloidyAndMaximumAllele() local
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/ |
H A D | GenotypeLikelihoodCalculators.java | 237 …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()
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H A D | HomogeneousPloidyModel.java | 14 private final int ploidy; field in HomogeneousPloidyModel 25 public HomogeneousPloidyModel(final SampleList sampleList, final int ploidy) { in HomogeneousPloidyModel()
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H A D | GenotypeAlleleCounts.java | 90 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
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H A D | AlleleSubsettingUtils.java | 67 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()
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/dports/biology/freebayes/freebayes-1.3.5/src/ |
H A D | CNV.cpp | 11 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
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/dports/biology/bcftools/bcftools-1.14/plugins/ |
H A D | fixploidy.c | 41 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
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/dports/biology/bio-mocha/bcftools-1.14/plugins/ |
H A D | fixploidy.c | 41 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
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/afcalc/ |
H A D | AlleleFrequencyCalculator.java | 57 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
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/ |
H A D | SomaticReferenceConfidenceModel.java | 58 public ReferenceConfidenceResult calcGenotypeLikelihoodsOfRefVsAny(final int ploidy, in calcGenotypeLikelihoodsOfRefVsAny() 98 …public void doIndelRefConfCalc(final int ploidy, final byte[] ref, final ReadPileup pileup, final … in doIndelRefConfCalc()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ |
H A D | ReferenceConfidenceModel.java | 192 …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()
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/dports/biology/vt/vt-0.57721/ |
H A D | estimator.cpp | 41 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()
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H A D | decompose2.cpp | 203 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
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H A D | decompose.cpp | 233 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
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ |
H A D | PosteriorProbabilitiesUtils.java | 218 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()
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/dports/biology/bbmap/bbmap/current/var2/ |
H A D | VarFilter.java | 167 double totalMapqAvg, double readLengthAvg, int ploidy, ScafMap map, boolean considerNearby){ in passesFilter() 237 public String toString(double pairingRate, int ploidy){ in toString()
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/dports/biology/freebayes/freebayes-1.3.5/python/ |
H A D | hwe.py | 33 def hwe_sampling_probln(genotype, genotypes, ploidy): argument
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/dports/biology/bbmap/bbmap/current/gff/ |
H A D | GffLine.java | 138 …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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