| /dports/biology/wise/wise2.4.1/src/snp/ |
| H A D | genotype.dy | 310 char * allele2;
337 allele2 = runner;
342 if ( allele2 == NULL ) {
399 if( allele2[0] != first ) {
401 second = allele2[0];
410 if( allele2[0] != first && allele2[0] != second ) {
414 /* this is fine, allele2 is either first or second allele */
416 } else if( first != allele2[0] ) {
417 second = allele2[0];
421 (allele2[0] != first && allele2[0] != second) ) {
[all …]
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| /dports/biology/bamutil/bamUtil-1.0.15/libStatGen/general/ |
| H A D | GenotypeLists.cpp | 167 int al2 = list[id].allele2[i]; in PairwiseCheck()
189 int al2 = list[motid].allele2[i]; in PairwiseCheck()
207 int al2 = list[fatid].allele2[i]; in PairwiseCheck()
292 return allele1.Find(allele) != -1 || allele2.Find(allele) != -1; in Matches()
303 allele2.Swap(genotype, checked); in SaveGenotype()
314 (list[motid].Matches(j, list[child].allele2[k]) || list[child].allele2[k] == -1)) || in CheckTrio()
315 ((list[fatid].Matches(i, list[child].allele2[k]) || list[child].allele2[k] == -1) && in CheckTrio()
323 allele2.Dimension(genotypes); in Dimension()
329 allele2[genotype] = al2; in SetGenotype()
335 allele2.Delete(genotype); in Delete()
[all …]
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| H A D | PedigreeAlleles.h | 124 longint allele2(1); in BinaryCoded()
127 allele2 <<= two - 1; in BinaryCoded()
129 return allele1 | allele2; in BinaryCoded()
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| H A D | PedigreeLoader.cpp | 333 String allele1, allele2; in LoadMendel() local
475 allele2.Copy(phenotype, separator + 1, 8); in LoadMendel()
476 allele2.Trim(); in LoadMendel()
496 int two = info->alleleNumbers.Integer(allele2); in LoadMendel()
501 two = info->NewAllele(allele2); in LoadMendel()
509 (const char *) allele2); in LoadMendel()
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| H A D | GenotypeLists.h | 27 IntArray allele1, allele2;
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/ |
| H A D | ThetaVariantEvaluator.java | 86 for (String allele2 : alleleCounts.keySet()) { in update1()
87 if (allele1.compareTo(allele2) < 0) { in update1()
90 if (allele1 .compareTo(allele2) == 0) { in update1()
95 int allele2Count = alleleCounts.get(allele2); in update1()
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| /dports/biology/haplohseq/haplohseq-0.1.2/src/util/ |
| H A D | InputProcessor.cpp | 90 char allele2 = alleles[1][i]; in hetIndices() local
92 if (this->isNoCall(allele1) or this->isNoCall(allele2)) { in hetIndices()
96 if (allele1 != allele2) { in hetIndices()
454 char allele2 = phasedAlleles[1][posIndex]; in readBafInformativeGenotypesChr() local
455 if (allele1 == allele2 || gt == "./." || islower(allele1) || islower(allele2) ) { in readBafInformativeGenotypesChr()
642 char allele2 = phasedAlleles[1][posIndex]; in readVcfInformativeGenotypesChr() local
645 if (allele1 == allele2 || gt == "./." || islower(allele1) || islower(allele2) ) { in readVcfInformativeGenotypesChr()
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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 | 282 for ( int allele2 = 0; allele2 < knownCountsByAllele.length; allele2++ ) { in getDirichletPrior()
283 for ( int allele1 = 0; allele1 <= allele2; allele1++) { in getDirichletPrior()
289 counts[allele2] += 1; in getDirichletPrior()
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| /dports/biology/p5-BioPerl/BioPerl-1.7.7/t/data/ |
| H A D | alleles.fas | 5 >allele2
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| /dports/biology/bolt-lmm/BOLT-LMM_v2.3.4/src/ |
| H A D | SnpInfo.hpp | 33 std::string allele1, allele2; member in LMM::SnpInfo
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| H A D | SnpData.cpp | 775 if (!(iss >> chrom_str >> snp.ID >> snp.genpos >> snp.physpos >> snp.allele1 >> snp.allele2)) in readBimFile()
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| H A D | Bolt.cpp | 1679 << snp.allele1 << "\t" << snp.allele2; in computeWritePredBetas()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/ |
| H A D | FastaAlternateReferenceMaker.java | 259 final byte allele2 = genotype.getAllele(1).getBases()[0]; in getIUPACBase()
260 return new String(new byte[] {BaseUtils.basesToIUPAC(allele1, allele2)}); in getIUPACBase()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/funcotator/ |
| H A D | FuncotationMapUnitTest.java | 288 final Allele allele2 = Allele.create("TAC"); in testMultiAlleleicFuncotationMapCreation() local
289 …Assert.assertEquals(alleleFuncotationMapMap.get(allele2).get("TRANSCRIPT_ALPHA_2").get(0).getField… in testMultiAlleleicFuncotationMapCreation()
290 …Assert.assertEquals(alleleFuncotationMapMap.get(allele2).get("TRANSCRIPT_BRAVO_2").get(0).getField… in testMultiAlleleicFuncotationMapCreation()
291 …Assert.assertEquals(alleleFuncotationMapMap.get(allele2).get("TRANSCRIPT_CHARLIE_2").get(0).getFie… in testMultiAlleleicFuncotationMapCreation()
341 final Allele allele2 = Allele.create("TAC"); in testMultiAlleleicFuncotationMapCreation() local
342 …Assert.assertEquals(alleleFuncotationMapMap.get(allele2).get("TRANSCRIPT_ALPHA_2").get(0).getField… in testMultiAlleleicFuncotationMapCreation()
343 …Assert.assertEquals(alleleFuncotationMapMap.get(allele2).get("TRANSCRIPT_BRAVO_2").get(0).getField… in testMultiAlleleicFuncotationMapCreation()
344 …Assert.assertEquals(alleleFuncotationMapMap.get(allele2).get("TRANSCRIPT_CHARLIE_2").get(0).getFie… in testMultiAlleleicFuncotationMapCreation()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/bs_tools/ |
| H A D | casbar_calling.h | 980 int allele2 = 666; in doBsCalling() local
995 genotype2 = (allele1<<2)|allele2; in doBsCalling()
998 allele2 = h2; in doBsCalling()
1007 genotype1 = (allele1<<2)|allele2; in doBsCalling()
1031 if ((Dna)allele1 == 'C' && (Dna)allele2 == 'G') in doBsCalling()
1036 …alled && ((Dna)allele1 == 'C' || (Dna)allele1 == 'G' || (Dna)allele2 == 'C' || (Dna)allele2 == 'G'… in doBsCalling()
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| /dports/biology/p5-BioPerl/BioPerl-1.7.7/t/Align/ |
| H A D | SimpleAlign.t | 505 'allele2' => 'GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT',
529 -allele2 => $ls,
536 'allele2' => 'GGAT{C.-}{C.-}ATT{C.C}CT{A.C}CT',
549 -allele2 => $ls,
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| /dports/biology/seqan1/seqan-1.3.1/lib/samtools/bcftools/ |
| H A D | bcf.tex | 41 {\tt GT} & {\tt uint8\_t[n]} & {\tt phase\char60\char60 6 | allele1\char60\char60 3 | allele2} \\
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| /dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/bcftools/ |
| H A D | bcf.tex | 41 …n]} & {\tt missing\char60\char60 7 | phased\char60\char60 6 | allele1\char60\char60 3 | allele2} \\
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| /dports/biology/hisat2/hisat2-2.2.1/ |
| H A D | repeat.h | 568 const RepeatAllele<index_t>& allele2 = alleles2[positions2[j].alleleID]; variable
569 if(!allele2.compatible(adjLeft2, adjRight2))
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| /dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/ |
| H A D | SimpleAlign.pm | 2996 my ($refseq, $allele1, $allele2) =
2998 if (!$refseq || !$allele1 || !$allele2) {
3007 map{substr($_->seq, $column, 1)} ($refseq, $allele1, $allele2);
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| /dports/biology/vcftools/vcftools-0.1.16/src/cpp/ |
| H A D | variant_file_output.cpp | 936 int allele1, allele2; in calc_hap_r2() local
945 allele2 = GT2[ui].first; in calc_hap_r2()
950 allele2 = GT2[ui].second; in calc_hap_r2()
953 if ((allele1 < 0) || (allele2 < 0)) in calc_hap_r2()
956 if (allele1 == 0 && allele2 == 0){ in calc_hap_r2()
958 } else if (allele1 == 0 && allele2 != 0){ in calc_hap_r2()
960 } else if (allele1 != 0 && allele2 == 0){ in calc_hap_r2()
970 if (allele2 == 0) in calc_hap_r2()
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| /dports/biology/seqan1/seqan-1.3.1/apps/snp_store/ |
| H A D | snp_store.h | 1388 int allele2 = -1; // second most frequent allele
1405 allele2 = k;
1411 if(allele1==refAllele && allele2==refAllele)
1419 if(allele1==refAllele) mutAllele=allele2;
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/snp_store/ |
| H A D | snp_store.h | 2764 int allele2 = -1; // second most frequent allele
2781 allele2 = k;
2787 if(allele1==refAllele && allele2==refAllele)
2795 if(allele1==refAllele) mutAllele=allele2;
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| /dports/biology/plink/plink-ng-79b2df8c/1.9/ |
| H A D | plink_data.c | 11624 void init_recode_cmax0(char* allele1, char* allele2, char** cur_mk_allelesx, uint32_t* cmalen, char… in init_recode_cmax0() argument
11626 uintptr_t alen2 = strlen(allele2); in init_recode_cmax0()
11635 memcpy(cmaptr, allele2, alen2); in init_recode_cmax0()
11639 cmaptr = memcpyax(cmaptr, allele2, alen2, delim2); in init_recode_cmax0()
11640 memcpy(cmaptr, allele2, alen2); in init_recode_cmax0()
11644 void init_recode_cmax(char* allele1, char* allele2, char** cur_mk_allelesx, uint32_t* cmalen, char … in init_recode_cmax() argument
11646 uintptr_t alen2 = strlen(allele2); in init_recode_cmax()
11651 memcpyx(cmaptr, allele2, alen2, delimiter); in init_recode_cmax()
11653 cmaptr = memcpyax(cur_mk_allelesx[3], allele2, alen2, delim2); in init_recode_cmax()
11654 memcpyx(cmaptr, allele2, alen2, delimiter); in init_recode_cmax()
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| /dports/biology/hisat2/hisat2-2.2.1/evaluation/tests/HLA_novel/ |
| H A D | hisatgenotype_locus_prev.py | 2236 for allele2 in allele_rep_groups[allele]:
2237 gen_alleles.add(allele2)
|