/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/ |
H A D | PerAlleleCollection.java | 45 public void set(Allele allele, X value){ in set() 60 public void setRef(Allele allele, X value){ in setRef() 69 public void setAlt(Allele allele, X value){ in setAlt() 80 public X get(Allele allele){ in get() 102 public X getAlt(Allele allele){ in getAlt()
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/dports/biology/emboss/EMBOSS-6.6.0/ajax/ensembl/ |
H A D | ensgvgenotype.c | 560 AjPStr allele = NULL; in ensGvgenotypeNewCpy() local 632 AjPStr allele = NULL; in ensGvgenotypeNewIni() local 1241 AjPStr allele = NULL; in ensGvgenotypeAddGvgenotypecode() local 1307 AjPStr allele = NULL; in ensGvgenotypeTrace() local 1394 AjPStr allele = NULL; in ensGvgenotypeCalculateAllelenumber() local 1429 AjPStr allele = NULL; in ensGvgenotypeCalculateMemsize() local 1511 AjPStr allele = NULL; in ensGvgenotypeFetchAlleleNumber() local 1553 AjPStr allele = NULL; in ensGvgenotypeFetchAlleleString() local 1651 AjPStr allele = NULL; in ensGvgenotypecodeNewCpy() local 1714 AjPStr allele = NULL; in ensGvgenotypecodeNewIni() local [all …]
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/dports/biology/freebayes/freebayes-1.3.5/src/ |
H A D | Sample.cpp | 6 int Sample::observationCount(Allele& allele) { in observationCount() 14 double Sample::observationCountInclPartials(Allele& allele) { in observationCountInclPartials() 18 double Sample::partialObservationCount(Allele& allele) { in partialObservationCount() 60 int Sample::qualSum(Allele& allele) { in qualSum() 76 double Sample::partialQualSum(Allele& allele) { in partialQualSum() 94 int Samples::observationCount(Allele& allele) { in observationCount() 98 double Samples::observationCountInclPartials(Allele& allele) { in observationCountInclPartials() 102 double Samples::partialObservationCount(Allele& allele) { in partialObservationCount() 144 int Samples::qualSum(Allele& allele) { in qualSum() 156 double Samples::partialQualSum(Allele& allele) { in partialQualSum() [all …]
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H A D | Allele.cpp | 299 string stringForAllele(const Allele &allele) { in stringForAllele() 392 for (auto& allele : alleles) { in operator <<() local 400 for (auto& allele : alleles) { in operator <<() local 513 Allele& allele = **a; in countAlleles() local 559 Allele& allele = *a; in countAlleles() local 573 Allele& allele = **a; in countAlleles() local 588 Allele*& allele = *a; in groupAllelesBySample() local 605 Allele*& allele = *a; in groupAllelesBySample() local 620 Allele& allele = *g->second.front(); in homogenizeAlleles() local 1494 bool isEmptyAllele(const Allele& allele) { in isEmptyAllele() [all …]
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H A D | Genotype.cpp | 59 int Genotype::alleleCount(Allele& allele) { in alleleCount() 207 bool Genotype::containsAllele(Allele& allele) { in containsAllele() 367 const AlleleCounter& allele = f->second; in numberOfAlleles() local 436 int GenotypeCombo::alleleCount(Allele& allele) { in alleleCount() 516 const Allele& allele = **a; in updateCachedCounts() local 566 const Allele& allele = **a; in updateCachedCounts() local 615 const AlleleCounter& allele = a->second; in countFrequencies() local 630 const AlleleCounter& allele = a->second; in counts() local 649 const AlleleCounter& allele = a->second; in observationCounts() local 1315 Allele& allele = *a; in addAllHomozygousCombos() local [all …]
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H A D | AlleleParser.cpp | 1860 Allele& allele = *a; in registerAlignment() local 1889 Allele& allele = *a; in registerAlignment() local 2530 Allele* allele = *a; local 2550 Allele* allele = *a; local 2594 Allele* allele = *a; local 2605 Allele* allele = *a; local 3212 Allele& allele = *a; local 3274 Allele& allele = *a; local 3697 Allele& allele = **a; local 3860 Allele& allele = **a; local [all …]
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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 | AFCalculationResult.java | 96 public int getAlleleCountAtMLE(final Allele allele) { in getAlleleCountAtMLE() 136 public boolean passesThreshold(final Allele allele, final double phredScaleQualThreshold) { in passesThreshold() 162 public double getLog10PosteriorOfAlleleAbsent(final Allele allele) { in getLog10PosteriorOfAlleleAbsent()
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/dports/biology/lamarc/lamarc-2.1.8/src/datalike/ |
H A D | haplotypes.cpp | 98 for (size_t allele=0; allele<((*dlList).size()-1); allele++) in CollapseHaplotypeDLs() local 240 for (unsigned long allele=0; allele<m_haplotype_alleles[res].size(); allele++) in GetAlleles() local 342 for (size_t allele=0; allele<m_haplotype_dlcells[set].size(); allele++) in PrintCellsAndAlleles() local 353 for (size_t allele=0; allele<m_haplotype_dlcells[set].size(); allele++) in PrintCellsAndAlleles() local
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/dports/biology/vcflib/vcflib-1.0.2/src/ |
H A D | vcfroc.cpp | 352 VariantAllele& allele = **va; in main() local 369 VariantAllele& allele = **va; in main() local 386 VariantAllele& allele = **va; in main() local 415 VariantAllele& allele = **va; in main() local 431 VariantAllele& allele = **va; in main() local 447 VariantAllele& allele = **va; in main() local
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/dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/ |
H A D | vcfroc.cpp | 342 VariantAllele& allele = **va; in main() local 359 VariantAllele& allele = **va; in main() local 376 VariantAllele& allele = **va; in main() local 405 VariantAllele& allele = **va; in main() local 421 VariantAllele& allele = **va; in main() local 437 VariantAllele& allele = **va; in main() local
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/dports/biology/freebayes/freebayes-1.3.5/vcflib/src/ |
H A D | vcfroc.cpp | 342 VariantAllele& allele = **va; in main() local 359 VariantAllele& allele = **va; in main() local 376 VariantAllele& allele = **va; in main() local 405 VariantAllele& allele = **va; in main() local 421 VariantAllele& allele = **va; in main() local 437 VariantAllele& allele = **va; in main() local
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/genotyper/ |
H A D | AlleleList.java | 32 int indexOfAllele(final A allele); in indexOfAllele() 45 default boolean containsAllele(final A allele){ in containsAllele()
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H A D | IndexedAlleleList.java | 66 public int indexOfAllele(final A allele) { in indexOfAllele()
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/dports/biology/lamarc/lamarc-2.1.8/src/convModel/ |
H A D | gc_trait.cpp | 36 gcTraitInfo::AddAllele(const gcTraitAllele& allele) in AddAllele() 46 gcTraitInfo::RemoveAllele(const gcTraitAllele& allele) in RemoveAllele()
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/dports/biology/bamutil/bamUtil-1.0.15/libStatGen/general/ |
H A D | PedigreeAlleles.h | 150 void Intersect(char allele) in Intersect() 158 bool AddAllele(char allele) in AddAllele()
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/dports/biology/freebayes/freebayes-1.3.5/contrib/freebayes/ |
H A D | GenotypePriors.cpp | 55 …uble probabilityGenotypeComboGivenAlleleFrequencyln(GenotypeCombo& genotypeCombo, Allele& allele) { in probabilityGenotypeComboGivenAlleleFrequencyln() 100 const string& allele = *a; in genotypeCombinationPriorProbability() local
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/dports/biology/vt/vt-0.57721/ |
H A D | decompose_blocksub.cpp | 162 char** allele = bcf_get_allele(v); in decompose_blocksub() local 223 char** allele = bcf_get_allele(v); in decompose_blocksub() local 289 char** allele = bcf_get_allele(v); in decompose_blocksub() local
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H A D | variant.cpp | 217 char** allele = bcf_get_allele(v); in classify() local 488 char** allele = bcf_get_allele(v); in update_vntr_from_info_fields() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/snputil/ |
H A D | snp_utils.cpp | 276 for(auto& allele: Alleles) { in GetAlleles() local 282 bool NSnp::IsSnpKnown( CScope &scope, const CMappedFeat &private_snp, const string &allele) in IsSnpKnown() 288 bool NSnp::IsSnpKnown( CScope& scope, const CSeq_loc& loc, const string & allele) in IsSnpKnown()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/ |
H A D | GenotypingData.java | 78 public int indexOfAllele(final A allele) { in indexOfAllele()
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H A D | GenotypingLikelihoods.java | 96 public int indexOfAllele(final A allele) { in indexOfAllele()
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/dports/biology/bbmap/bbmap/current/var2/ |
H A D | VarKey.java | 55 int allele; field in VarKey
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/dports/biology/stacks/stacks-2.4/src/ |
H A D | kmers.cc | 237 vector<pair<allele_type, string> >::iterator allele; in populate_kmer_hash() local 287 vector<pair<allele_type, string> >::iterator allele; in populate_kmer_hash() local 347 vector<pair<allele_type, string> >::iterator allele; in populate_kmer_hash() local 434 int dist(const char *tag_1, Locus *tag_2, allele_type allele) { in dist() 648 check_frameshift(const char *tag_1, Locus *tag_2, allele_type allele, size_t mismatches) in check_frameshift()
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/dports/biology/hisat2/hisat2-2.2.1/ |
H A D | repeat.h | 343 RepeatAllele<index_t>& allele = repeat.alleles[positions[p].alleleID]; in construct() local 406 const RepeatAllele<index_t>& allele = alleles[position.alleleID]; variable 476 const RepeatAllele<index_t>& allele = alleles[position.alleleID]; variable 555 const RepeatAllele<index_t>& allele = alleles[positions[i].alleleID]; variable
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ |
H A D | PerAlleleAnnotation.java | 47 private boolean includeAllele(final Allele allele) { in includeAllele()
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