Home
last modified time | relevance | path

Searched defs:allele (Results 1 – 25 of 160) sorted by relevance

1234567

/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/
H A DPerAlleleCollection.java45 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()
/dports/biology/emboss/EMBOSS-6.6.0/ajax/ensembl/
H A Densgvgenotype.c560 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 …]
/dports/biology/freebayes/freebayes-1.3.5/src/
H A DSample.cpp6 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 …]
H A DAllele.cpp299 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 …]
H A DGenotype.cpp59 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 …]
H A DAlleleParser.cpp1860 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 …]
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/afcalc/
H A DAFCalculationResult.java96 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()
/dports/biology/lamarc/lamarc-2.1.8/src/datalike/
H A Dhaplotypes.cpp98 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
/dports/biology/vcflib/vcflib-1.0.2/src/
H A Dvcfroc.cpp352 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
/dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/
H A Dvcfroc.cpp342 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
/dports/biology/freebayes/freebayes-1.3.5/vcflib/src/
H A Dvcfroc.cpp342 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
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/genotyper/
H A DAlleleList.java32 int indexOfAllele(final A allele); in indexOfAllele()
45 default boolean containsAllele(final A allele){ in containsAllele()
H A DIndexedAlleleList.java66 public int indexOfAllele(final A allele) { in indexOfAllele()
/dports/biology/lamarc/lamarc-2.1.8/src/convModel/
H A Dgc_trait.cpp36 gcTraitInfo::AddAllele(const gcTraitAllele& allele) in AddAllele()
46 gcTraitInfo::RemoveAllele(const gcTraitAllele& allele) in RemoveAllele()
/dports/biology/bamutil/bamUtil-1.0.15/libStatGen/general/
H A DPedigreeAlleles.h150 void Intersect(char allele) in Intersect()
158 bool AddAllele(char allele) in AddAllele()
/dports/biology/freebayes/freebayes-1.3.5/contrib/freebayes/
H A DGenotypePriors.cpp55 …uble probabilityGenotypeComboGivenAlleleFrequencyln(GenotypeCombo& genotypeCombo, Allele& allele) { in probabilityGenotypeComboGivenAlleleFrequencyln()
100 const string& allele = *a; in genotypeCombinationPriorProbability() local
/dports/biology/vt/vt-0.57721/
H A Ddecompose_blocksub.cpp162 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
H A Dvariant.cpp217 char** allele = bcf_get_allele(v); in classify() local
488 char** allele = bcf_get_allele(v); in update_vntr_from_info_fields() local
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/snputil/
H A Dsnp_utils.cpp276 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()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/
H A DGenotypingData.java78 public int indexOfAllele(final A allele) { in indexOfAllele()
H A DGenotypingLikelihoods.java96 public int indexOfAllele(final A allele) { in indexOfAllele()
/dports/biology/bbmap/bbmap/current/var2/
H A DVarKey.java55 int allele; field in VarKey
/dports/biology/stacks/stacks-2.4/src/
H A Dkmers.cc237 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()
/dports/biology/hisat2/hisat2-2.2.1/
H A Drepeat.h343 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
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/
H A DPerAlleleAnnotation.java47 private boolean includeAllele(final Allele allele) { in includeAllele()

1234567