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/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() argument
49 if (allele.isReference()){ in set()
50 setRef(allele, value); in set()
52 setAlt(allele, value); in set()
65 refAllele = Optional.of(allele); in setRef()
73 altAlleleValueMap.put(allele, value); in setAlt()
80 public X get(Allele allele){ in get() argument
82 if (allele.isReference()){ in get()
86 return getAlt(allele); in get()
102 public X getAlt(Allele allele){ in getAlt() argument
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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/etc/
H A Dfeature_keys8 -10_signal allele citation db_xref experiment gene gene_synonym inference locus_tag map note o…
9 -35_signal allele citation db_xref experiment gene gene_synonym inference locus_tag map note o…
12 CAAT_signal allele citation db_xref experiment gene gene_synonym inference locus_tag map note o…
15 D-loop allele citation db_xref experiment gene gene_synonym inference locus_tag map note o…
17 GC_signal allele citation db_xref experiment gene gene_synonym inference locus_tag map note o…
22 STS allele citation db_xref experiment gene gene_synonym inference locus_tag map note o…
24 TATA_signal allele citation db_xref experiment gene gene_synonym inference locus_tag map note o…
48 operon @operon allele citation db_xref experiment function inference map note phenotype ps…
50 polyA_signal allele citation db_xref experiment gene gene_synonym inference locus_tag map note o…
51 polyA_site allele citation db_xref experiment gene gene_synonym inference locus_tag map note o…
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/dports/biology/freebayes/freebayes-1.3.5/python/
H A Dallelebayes.py39 for allele in genotype:
63 for allele in alleles:
64 alt = allele['alt']
72 for allele in alleles:
73 allele['quality'] = phred.phred2ln(allele['quality'])
93 if allele == key:
145 for allele, count in genotype if allele_groups.has_key(allele)])
169 true_alleles = [{'alt':allele} for allele in true_allele_permutation]
205 result -= sum([math.log(math.factorial(allele[1])) for allele in genotype])
282 return fold(operator.add, [allele * count for allele, count in genotype])
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/dports/biology/vcflib/vcflib-1.0.2/src/
H A Dvcfroc.cpp353 if (allele.ref.size() == 1 && allele.ref.size() == allele.alt.size()) { in main()
355 } else if (allele.ref.size() != allele.alt.size()) { in main()
370 if (allele.ref.size() == 1 && allele.ref.size() == allele.alt.size()) { in main()
372 } else if (allele.ref.size() != allele.alt.size()) { in main()
387 if (allele.ref.size() == 1 && allele.ref.size() == allele.alt.size()) { in main()
390 } else if (allele.ref.size() != allele.alt.size()) { in main()
416 if (allele.ref.size() == 1 && allele.ref.size() == allele.alt.size()) { in main()
419 } else if (allele.ref.size() != allele.alt.size()) { in main()
432 if (allele.ref.size() == 1 && allele.ref.size() == allele.alt.size()) { in main()
435 } else if (allele.ref.size() != allele.alt.size()) { in main()
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/dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/
H A Dvcfroc.cpp343 if (allele.ref.size() == 1 && allele.ref.size() == allele.alt.size()) { in main()
345 } else if (allele.ref.size() != allele.alt.size()) { in main()
360 if (allele.ref.size() == 1 && allele.ref.size() == allele.alt.size()) { in main()
362 } else if (allele.ref.size() != allele.alt.size()) { in main()
377 if (allele.ref.size() == 1 && allele.ref.size() == allele.alt.size()) { in main()
380 } else if (allele.ref.size() != allele.alt.size()) { in main()
406 if (allele.ref.size() == 1 && allele.ref.size() == allele.alt.size()) { in main()
409 } else if (allele.ref.size() != allele.alt.size()) { in main()
422 if (allele.ref.size() == 1 && allele.ref.size() == allele.alt.size()) { in main()
425 } else if (allele.ref.size() != allele.alt.size()) { in main()
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/dports/biology/freebayes/freebayes-1.3.5/vcflib/src/
H A Dvcfroc.cpp343 if (allele.ref.size() == 1 && allele.ref.size() == allele.alt.size()) { in main()
345 } else if (allele.ref.size() != allele.alt.size()) { in main()
360 if (allele.ref.size() == 1 && allele.ref.size() == allele.alt.size()) { in main()
362 } else if (allele.ref.size() != allele.alt.size()) { in main()
377 if (allele.ref.size() == 1 && allele.ref.size() == allele.alt.size()) { in main()
380 } else if (allele.ref.size() != allele.alt.size()) { in main()
406 if (allele.ref.size() == 1 && allele.ref.size() == allele.alt.size()) { in main()
409 } else if (allele.ref.size() != allele.alt.size()) { in main()
422 if (allele.ref.size() == 1 && allele.ref.size() == allele.alt.size()) { in main()
425 } else if (allele.ref.size() != allele.alt.size()) { in main()
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/dports/biology/emboss/EMBOSS-6.6.0/ajax/ensembl/
H A Densgvgenotype.c206 if (!allele) in gvHaplotypeNewIni()
560 AjPStr allele = NULL; in ensGvgenotypeNewCpy() local
632 AjPStr allele = NULL; in ensGvgenotypeNewIni() local
1160 if (!allele) in ensGvgenotypeAddAllele()
1199 if (!allele) in ensGvgenotypeAddAllelenumber()
1258 if (allele) in ensGvgenotypeAddGvgenotypecode()
1444 if (allele) in ensGvgenotypeCalculateMemsize()
1676 if (allele) in ensGvgenotypecodeNewCpy()
1736 if (allele) in ensGvgenotypecodeNewIni()
2070 if (!allele) in ensGvgenotypecodeAddAllele()
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/dports/biology/freebayes/freebayes-1.3.5/src/
H A DAllele.cpp330 for (vector<Allele>::iterator allele = alleles.begin(); allele != alleles.end(); allele++) { in stringForAlleles() local
346 string tojson(Allele*& allele) { return allele->tojson(); } in tojson() argument
407 out << *allele; in operator <<()
501 … for (vector<Allele*>::iterator allele = alleles.begin() + 1; allele != alleles.end(); ++allele) { in areHomozygous() local
589 groups[allele->sampleID].push_back(allele); in groupAllelesBySample()
606 groups[allele->sampleID].push_back(allele); in groupAllelesBySample()
673 …for (vector<Allele*>::iterator allele = sample->second.begin(); allele != sample->second.end(); ++… in groupAlleles() local
674 alleleGroups[(*allele)->currentBase].push_back(*allele); in groupAlleles()
912 for (list<Allele*>::iterator allele = alleles.begin(); allele != alleles.end(); ++allele) { in filterAlleles() local
1509 if (allele.isReference() || allele.isSNP() || allele.isMNP()) { in isUnflankedIndel()
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H A DAlleleParser.cpp1904 allele.readMismatchRate = indelRate + allele.readSNPRate; in registerAlignment()
1911 allele.readMismatchRate = allele.readIndelRate + snpRate; in registerAlignment()
2099 … for (vector<Allele>::iterator allele = ra.alleles.begin(); allele != ra.alleles.end(); ++allele) { local
2164 for (vector<Allele*>::iterator allele = alleles.begin(); allele != alleles.end(); ++allele) { local
2435 …inputVariantAlleles[bamMultiReader.GETREFID(allele.referenceName)][allele.position].push_back(alle…
2583 for (vector<Allele*>::iterator allele = alleles.begin(); allele != alleles.end(); ++allele) { local
3726 if (allele.quality >= parameters.BQL0 && allele.currentBase != "N"
3729 samples[allele.sampleID][allele.currentBase].push_back(*a);
3826 allele->update();
3827 return allele;
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H A DSample.h60 bool observationSupports(Allele* obs, Allele* allele);
63 int observationCount(Allele& allele);
64 double observationCountInclPartials(Allele& allele);
65 double partialObservationCount(Allele& allele);
79 int qualSum(Allele& allele);
81 double partialQualSum(Allele& allele);
109 int observationCount(Allele& allele);
110 double observationCountInclPartials(Allele& allele);
111 double partialObservationCount(Allele& allele);
117 int qualSum(Allele& allele);
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H A DGenotype.cpp33 Allele& b = i->allele; in alternateAlleles()
43 Allele& b = i->allele; in alternateBases()
98 Allele& b = i->allele; in relativeGenotype()
128 Allele& b = i->allele; in relativeGenotype()
156 Allele& b = i->allele; in relativeGenotype()
346 if (ai->allele != bi->allele) in operator <()
347 return ai->allele < bi->allele; in operator <()
398 if (allele.basesLeft >= allele.basesRight) { in init()
522 if (allele.basesLeft >= allele.basesRight) { in updateCachedCounts()
572 if (allele.basesLeft >= allele.basesRight) { in updateCachedCounts()
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H A DSample.cpp6 int Sample::observationCount(Allele& allele) { in observationCount() argument
7 return observationCount(allele.currentBase); in observationCount()
60 int Sample::qualSum(Allele& allele) { in qualSum() argument
61 return qualSum(allele.currentBase); in qualSum()
76 double Sample::partialQualSum(Allele& allele) { in partialQualSum() argument
77 return partialQualSum(allele.currentBase); in partialQualSum()
94 int Samples::observationCount(Allele& allele) { in observationCount() argument
144 int Samples::qualSum(Allele& allele) { in qualSum() argument
145 return qualSum(allele.currentBase); in qualSum()
157 return partialQualSum(allele.currentBase); in partialQualSum()
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/dports/biology/bbmap/bbmap/current/var2/
H A DVarKey.java9 return new VarKey(v.scafnum, v.start, v.allele.length, v.type, v.allele[0]); in toVarKey()
13 return new VarKey(v.scafnum, v.start, v.reflen(), v.type, v.allele[0]); in toVarKey()
21 allele=allele_; in VarKey()
26 …tart, 4)^Integer.rotateRight(start, 18)^Integer.rotateLeft(type, 8)^Integer.rotateLeft(allele, 12); in hashCode()
36 …eturn scafNum==b.scafNum && start==b.start && length==b.length && type==b.type && allele==b.allele; in equals()
46 if(allele!=b.allele){return allele-b.allele;} in compareTo()
55 int allele; field in VarKey
/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() argument
97 Utils.nonNull(allele); in getAlleleCountAtMLE()
98 …Utils.validate( allele.isNonReference(), () -> "Cannot get the alt allele index for reference alle… in getAlleleCountAtMLE()
99 final int indexInAllAllelesIncludingRef = allelesUsedInGenotyping.indexOf(allele); in getAlleleCountAtMLE()
136 public boolean passesThreshold(final Allele allele, final double phredScaleQualThreshold) { in passesThreshold() argument
137 Utils.nonNull(allele); in passesThreshold()
138 …return getLog10PosteriorOfAlleleAbsent(allele) + EPSILON < QualityUtils.qualToErrorProbLog10(phred… in passesThreshold()
162 public double getLog10PosteriorOfAlleleAbsent(final Allele allele) { in getLog10PosteriorOfAlleleAbsent() argument
163 Utils.nonNull(allele); in getLog10PosteriorOfAlleleAbsent()
164 final Double log10pNonRef = log10pRefByAllele.get(allele); in getLog10PosteriorOfAlleleAbsent()
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/dports/biology/vt/vt-0.57721/
H A Dvariant_manip.cpp248 char* ref = allele[0]; in classify_variant()
262 if (strchr(allele[i],'<')) in classify_variant()
268 … if (allele[i][0]=='<' && allele[i][1]=='V' && allele[i][2]=='N' && allele[i][len-1]=='>' ) in classify_variant()
272 if (allele[i][j]<'0' || allele[i][j]>'9') in classify_variant()
281 … allele[i][1]=='V' && allele[i][2]=='N' && allele[i][3]=='T' && allele[i][4]=='R' && in classify_variant()
289 allele[i][1]=='S' && allele[i][2]=='T' && allele[i][3]=='R' && in classify_variant()
295 … else if (allele[i][0]=='<' && allele[i][1]=='S' && allele[i][2]=='T' && allele[i][len-1]=='>' ) in classify_variant()
301 if ((allele[i][j]<'0' || allele[i][j]>'9') && allele[i][j]!='.') in classify_variant()
324 else if (strchr(allele[i],'[')||strchr(allele[i],']')) in classify_variant()
332 else if (allele[i][0]=='.' || strcmp(allele[i],allele[0])==0) in classify_variant()
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H A Dvariant.cpp222 char* ref = allele[0]; in classify()
236 if (strchr(allele[i],'<')) in classify()
242 … if (allele[i][0]=='<' && allele[i][1]=='V' && allele[i][2]=='N' && allele[i][len-1]=='>' ) in classify()
246 if (allele[i][j]<'0' || allele[i][j]>'9') in classify()
255 … allele[i][1]=='V' && allele[i][2]=='N' && allele[i][3]=='T' && allele[i][4]=='R' && in classify()
263 allele[i][1]=='S' && allele[i][2]=='T' && allele[i][3]=='R' && in classify()
269 … else if (allele[i][0]=='<' && allele[i][1]=='S' && allele[i][2]=='T' && allele[i][len-1]=='>' ) in classify()
275 if ((allele[i][j]<'0' || allele[i][j]>'9') && allele[i][j]!='.') in classify()
298 else if (strchr(allele[i],'[')||strchr(allele[i],']')) in classify()
306 else if (allele[i][0]=='.' || strcmp(allele[i],allele[0])==0) in classify()
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/dports/biology/hisat2/hisat2-2.2.1/evaluation/tests/genotype_genome/
H A Dhisatgenotype_prev.py159 for allele in alleles:
160 if allele not in allele_vars:
161 allele_vars[allele] = set()
162 allele_vars[allele].add(var_id)
651 HLA_counts = [[allele, count] for allele, count in HLA_counts.items()]
680 prob[allele] = mass / length[allele] / total
685 if allele in prob2:
686 diff += abs(prob1[allele] - prob2[allele])
706 for allele in alleles:
730 … HLA_prob_next[allele] += (float(count) * HLA_prob[allele] / alleles_prob)
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/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
100 if (!((*dlList)[allele] == (*dlComp)[allele])) in CollapseHaplotypeDLs()
240 for (unsigned long allele=0; allele<m_haplotype_alleles[res].size(); allele++) in GetAlleles() local
242 retvec.push_back(m_haplotype_alleles[res][allele]); in GetAlleles()
342 for (size_t allele=0; allele<m_haplotype_dlcells[set].size(); allele++) in PrintCellsAndAlleles() local
345 CellToData(m_haplotype_dlcells[set][allele][0], 0) in PrintCellsAndAlleles()
353 for (size_t allele=0; allele<m_haplotype_dlcells[set].size(); allele++) in PrintCellsAndAlleles() local
355 cout << m_haplotype_dlcells[set][allele][0]->DLsToString(0,0); in PrintCellsAndAlleles()
/dports/biology/bamutil/bamUtil-1.0.15/libStatGen/general/
H A DPedigreeAlleles.h150 void Intersect(char allele) in Intersect() argument
152 if (one != allele && two != allele) in Intersect()
155 one = two = allele; in Intersect()
158 bool AddAllele(char allele) in AddAllele() argument
160 if (one == allele || two == allele) in AddAllele()
166 if (one == 0) one = allele; in AddAllele()
167 else two = allele; in AddAllele()
/dports/biology/sra-tools/sra-tools-2.11.0/tools/cg-load/
H A Dfactory-evidence-intervals.c199 rc = str2buf(b, p - b, data->allele[0], sizeof(data->allele[0])); in CGEvidenceIntervals15_Read()
202 rc = str2buf(b, p - b, data->allele[1], sizeof(data->allele[1])); in CGEvidenceIntervals15_Read()
205 rc = str2buf(b, p - b, data->allele[2], sizeof(data->allele[2])); in CGEvidenceIntervals15_Read()
216 data->allele_indexes, data->score, data->allele[0], data->allele[1], data->allele[2], in CGEvidenceIntervals15_Read()
251 rc = str2buf(b, p - b, data->allele[0], sizeof(data->allele[0])); in CGEvidenceIntervals20_Read()
254 rc = str2buf(b, p - b, data->allele[1], sizeof(data->allele[1])); in CGEvidenceIntervals20_Read()
257 rc = str2buf(b, p - b, data->allele[2], sizeof(data->allele[2])); in CGEvidenceIntervals20_Read()
260 rc = str2buf(b, p - b, data->allele[3], sizeof(data->allele[3])); in CGEvidenceIntervals20_Read()
276 data->allele[0], data->allele[1], data->allele[2], data->allele[3], in CGEvidenceIntervals20_Read()
/dports/biology/vcflib/vcflib-1.0.2/doc/
H A DbFst.md14 …subpopulation's allele frequency and Fis (fixation index, within each subpopulation), a free param…
26 3. Observed allele frequency in target.
27 4. Estimated allele frequency in target.
28 5. Observed allele frequency in background.
29 6. Estimated allele frequency in background.
30 7. Observed allele frequency combined.
31 8. Estimated allele frequency in combined.
39 required: d,deltaaf -- skip sites were the difference in allele frequency is less than deltaaf
/dports/biology/bio-mocha/bcftools-1.14/
H A Dconsensus.c118 int argc, output_iupac, haplotype, allele, isample, napplied; member
238 if ( (args->haplotype || args->allele) && args->isample<0 ) in init_data()
512 if ( args->allele==PICK_IUPAC ) in apply_variant()
563 int l = strlen(rec->d.allele[jalt]); in apply_variant()
644 int l = strlen(rec->d.allele[i]); in apply_variant()
678 alleles[0] = rec->d.allele[0][0]; in apply_variant()
693 if ( rec->d.allele[0][0] == rec->d.allele[ialt][0] ) in apply_variant()
723 char *alt_allele = rec->d.allele[ialt]; in apply_variant()
849 mark_ins(rec->d.allele[0], alt_allele, args->mark_ins); in apply_variant()
851 mark_snv(rec->d.allele[0], alt_allele, args->mark_snv); in apply_variant()
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/dports/biology/bcftools/bcftools-1.14/
H A Dconsensus.c118 int argc, output_iupac, haplotype, allele, isample, napplied; member
238 if ( (args->haplotype || args->allele) && args->isample<0 ) in init_data()
512 if ( args->allele==PICK_IUPAC ) in apply_variant()
563 int l = strlen(rec->d.allele[jalt]); in apply_variant()
644 int l = strlen(rec->d.allele[i]); in apply_variant()
678 alleles[0] = rec->d.allele[0][0]; in apply_variant()
693 if ( rec->d.allele[0][0] == rec->d.allele[ialt][0] ) in apply_variant()
723 char *alt_allele = rec->d.allele[ialt]; in apply_variant()
849 mark_ins(rec->d.allele[0], alt_allele, args->mark_ins); in apply_variant()
851 mark_snv(rec->d.allele[0], alt_allele, args->mark_snv); in apply_variant()
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/dports/biology/py-pysam/pysam-0.18.0/bcftools/
H A Dconsensus.c118 int argc, output_iupac, haplotype, allele, isample, napplied; member
238 if ( (args->haplotype || args->allele) && args->isample<0 ) in init_data()
512 if ( args->allele==PICK_IUPAC ) in apply_variant()
563 int l = strlen(rec->d.allele[jalt]); in apply_variant()
644 int l = strlen(rec->d.allele[i]); in apply_variant()
678 alleles[0] = rec->d.allele[0][0]; in apply_variant()
693 if ( rec->d.allele[0][0] == rec->d.allele[ialt][0] ) in apply_variant()
723 char *alt_allele = rec->d.allele[ialt]; in apply_variant()
849 mark_ins(rec->d.allele[0], alt_allele, args->mark_ins); in apply_variant()
851 mark_snv(rec->d.allele[0], alt_allele, args->mark_snv); in apply_variant()
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H A Dconsensus.c.pysam.c120 int argc, output_iupac, haplotype, allele, isample, napplied; member
240 if ( (args->haplotype || args->allele) && args->isample<0 ) in init_data()
514 if ( args->allele==PICK_IUPAC ) in apply_variant()
565 int l = strlen(rec->d.allele[jalt]); in apply_variant()
646 int l = strlen(rec->d.allele[i]); in apply_variant()
680 alleles[0] = rec->d.allele[0][0]; in apply_variant()
695 if ( rec->d.allele[0][0] == rec->d.allele[ialt][0] ) in apply_variant()
725 char *alt_allele = rec->d.allele[ialt]; in apply_variant()
851 mark_ins(rec->d.allele[0], alt_allele, args->mark_ins); in apply_variant()
853 mark_snv(rec->d.allele[0], alt_allele, args->mark_snv); in apply_variant()
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