/dports/biology/mapm3/mapm3-3.0_1/quant/ |
H A D | qlow.h | 30 #define for_locus_genotypes(data_type,geno) \ argument 31 for (geno=0; geno<(data_type==BACKCROSS ? 2:3); geno++) 44 #define for_interval_genotypes(data_type,geno) \ argument 45 for (geno=0; geno<(data_type==BACKCROSS ? 4:9); geno++)
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H A D | qdata.c | 142 int geno, num; local 149 for_interval_genotypes(raw.data_type,geno) 151 data->genotype[data_i][interval][num++]=geno; 283 GENOTYPE geno, k; local 297 for (geno=(GENOTYPE)i, j=0; j<num_intervals; j++, geno>>=1) { 311 for (geno=i, j=0; j<num_intervals; j++, geno/=3) { 313 this_genotype= ((int)geno)%3; 400 int j, k, geno, qtl, left, right; local 432 for_interval_genotypes(raw.data_type,geno) { 433 left= left_genotype[geno]; [all …]
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H A D | qctm.c | 401 indiv_rec_like[j][geno][poss_genotype[j]]+=rec_like[j][geno]; 437 indiv_rec_like[j][geno][qtl]; 527 int j, y, n, c, geno; local 542 geno= poss_geno[j][y]; 544 trans_prob[j][geno][qtl_genotype[j]] * indiv_prob[j][geno]; 559 geno= poss_geno[j][y]; 560 rec_like[j][geno] *= ratio; 583 int j, geno, qtl, left, right; local 592 left= left_genotype[geno]; 593 right= right_genotype[geno]; [all …]
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/dports/biology/vt/vt-0.57721/ |
H A D | profile_chm1.cpp | 79 int32_t geno[4][4]; member in __anonee2a309b0111::ConcordanceStats 87 geno[i][j] = 0; in ConcordanceStats() 529 ++concordance[i].geno[x][y]; in profile_chm1() 609 int32_t (&geno)[4][4] = concordance[i].geno; in print_stats() local 616 total += geno[i][j]; in print_stats() 619 concordance += geno[i][j]; in print_stats() 628 …fprintf(stderr, " R/R %8d %8d %8d %8d\n", geno[0][0], geno[0][1], geno[0][2], geno[0][3]); in print_stats() 629 …fprintf(stderr, " R/A %8d %8d %8d %8d\n", geno[1][0], geno[1][1], geno[1][2], geno[1][3]); in print_stats() 630 …fprintf(stderr, " A/A %8d %8d %8d %8d\n", geno[2][0], geno[2][1], geno[2][2], geno[2][3]); in print_stats() 631 …fprintf(stderr, " ./. %8d %8d %8d %8d\n", geno[3][0], geno[3][1], geno[3][2], geno[3][3]); in print_stats()
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H A D | profile_na12878.cpp | 84 int32_t geno[4][4]; member in __anon2565e3eb0111::ConcordanceStats 92 geno[i][j] = 0; in ConcordanceStats() 605 ++concordance[i].geno[xt][yt]; in profile_na12878() 690 ++concordance[i].geno[xt][yt]; in profile_na12878() 771 ++concordance[i].geno[xt][yt]; in profile_na12878() 908 int32_t (&geno)[4][4] = concordance[i].geno; in print_stats() local 915 total += geno[i][j]; in print_stats() 927 …fprintf(stderr, " R/R %8d %8d %8d %8d\n", geno[0][0], geno[0][1], geno[0][2], geno[0][3]); in print_stats() 928 …fprintf(stderr, " R/A %8d %8d %8d %8d\n", geno[1][0], geno[1][1], geno[1][2], geno[1][3]); in print_stats() 929 …fprintf(stderr, " A/A %8d %8d %8d %8d\n", geno[2][0], geno[2][1], geno[2][2], geno[2][3]); in print_stats() [all …]
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/dports/biology/bamutil/bamUtil-1.0.15/libStatGen/general/ |
H A D | Pedigree.cpp | 572 int fat1 = fat.hasAllele(geno.one); in AutosomalCheck() 573 int fat2 = fat.hasAllele(geno.two); in AutosomalCheck() 604 if (haplos[geno.one] != i) in AutosomalCheck() 607 haplos[geno.one] = i; in AutosomalCheck() 609 if (haplos[geno.two] != i) in AutosomalCheck() 612 haplos[geno.two] = i; in AutosomalCheck() 621 counts[geno.one]++; in AutosomalCheck() 622 if (geno.isHomozygous()) in AutosomalCheck() 625 counts[geno.two]++; in AutosomalCheck() 833 inferred_father.Intersect(mot1 ? geno.two : geno.one); in SexLinkedCheck() [all …]
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/dports/biology/gemma/GEMMA-0.98.3/src/ |
H A D | gemma_io.cpp | 757 if (geno >= 0 && geno <= 0.5) { in ReadFile_geno() 760 if (geno > 0.5 && geno < 1.5) { in ReadFile_geno() 763 if (geno >= 1.5 && geno <= 2.0) { in ReadFile_geno() 778 maf += geno; in ReadFile_geno() 888 double v_x, v_w, geno; in ReadFile_bed() local 1790 geno = 0; in ReadFile_geno() 2034 if (geno == -9) { in ReadFile_bed() 2035 geno = 0; in ReadFile_bed() 2170 if (geno == -9) { in ReadFile_bed() 2841 gsl_blas_ddot(geno, geno, &geno_var); in BimbamKinUncentered() [all …]
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H A D | varcov.cpp | 266 gsl_vector *geno = gsl_vector_alloc(ni_test); in AnalyzeBimbam() local 308 gsl_vector_add_constant(geno, -1.0 * geno_mean); in AnalyzeBimbam() 310 for (size_t j = 0; j < geno->size; j++) { in AnalyzeBimbam() 311 x_vec[j] = gsl_vector_get(geno, j); in AnalyzeBimbam() 340 gsl_vector_free(geno); in AnalyzeBimbam() 366 gsl_vector *geno = gsl_vector_alloc(ni_test); in AnalyzePlink() local 407 Plink_ReadOneSNP(t2, indicator_idv, infile, geno, geno_mean); in AnalyzePlink() 408 gsl_vector_add_constant(geno, -1.0 * geno_mean); in AnalyzePlink() 410 for (size_t j = 0; j < geno->size; j++) { in AnalyzePlink() 411 x_vec[j] = gsl_vector_get(geno, j); in AnalyzePlink() [all …]
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H A D | prdt.cpp | 220 double geno, x_mean, x_train_mean, effect_size; in AnalyzeBimbam() local 257 geno = atof(ch_ptr); in AnalyzeBimbam() 258 x_train_mean += geno; in AnalyzeBimbam() 266 geno = atof(ch_ptr); in AnalyzeBimbam() 268 gsl_vector_set(x, c_phen, geno); in AnalyzeBimbam() 270 x_mean += geno; in AnalyzeBimbam() 286 geno = gsl_vector_get(x, i); in AnalyzeBimbam() 290 gsl_vector_set(x, i, geno - x_train_mean); in AnalyzeBimbam() 324 double geno, x_mean, x_train_mean, effect_size; in AnalyzePlink() local 423 geno = gsl_vector_get(x, i); in AnalyzePlink() [all …]
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/dports/biology/gemma/GEMMA-0.98.3/test/ |
H A D | test_suite.sh | 9 $gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \ 23 $gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \ 37 -g ../example/mouse_hs1940.geno.txt.gz \ 51 $gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \ 70 -g ../example/mouse_hs1940.geno.txt.gz \ 84 $gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \ 96 $gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \ 113 $gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \ 125 $gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \ 141 $gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \
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/dports/biology/vcflib/vcflib-1.0.2/src/ |
H A D | var.hpp | 66 virtual double unphred(map< string, vector<string> > & geno, int index) = 0; 98 double unphred(map< string, vector<string> > & geno, int index); 105 double unphred(map< string, vector<string> > & geno, int index); 112 double unphred(map< string, vector<string> > & geno, int index); 120 double unphred(map< string, vector<string> > & geno, int index);
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H A D | var.cpp | 130 double gt::unphred(map< string, vector<string> > & geno, int index){ in unphred() argument 134 double gl::unphred(map< string, vector<string> > & geno, int index){ in unphred() argument 136 double unphreded = atof(geno["GL"][index].c_str()); in unphred() 140 double gp::unphred(map< string, vector<string> > & geno, int index){ in unphred() argument 142 double unphreded = atof(geno["GP"][index].c_str()); in unphred() 146 double pl::unphred(map< string, vector<string> > & geno, int index){ in unphred() argument 148 double unphreded = atof(geno["PL"][index].c_str()); in unphred()
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/dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/ |
H A D | var.hpp | 57 virtual double unphred(map< string, vector<string> > & geno, int index) = 0; 89 double unphred(map< string, vector<string> > & geno, int index); 96 double unphred(map< string, vector<string> > & geno, int index); 103 double unphred(map< string, vector<string> > & geno, int index); 111 double unphred(map< string, vector<string> > & geno, int index);
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H A D | var.cpp | 112 double gt::unphred(map< string, vector<string> > & geno, int index){ in unphred() argument 116 double gl::unphred(map< string, vector<string> > & geno, int index){ in unphred() argument 118 double unphreded = atof(geno["GL"][index].c_str()); in unphred() 122 double gp::unphred(map< string, vector<string> > & geno, int index){ in unphred() argument 124 double unphreded = atof(geno["GP"][index].c_str()); in unphred() 128 double pl::unphred(map< string, vector<string> > & geno, int index){ in unphred() argument 130 double unphreded = atof(geno["PL"][index].c_str()); in unphred()
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/dports/biology/freebayes/freebayes-1.3.5/vcflib/src/ |
H A D | var.hpp | 57 virtual double unphred(map< string, vector<string> > & geno, int index) = 0; 89 double unphred(map< string, vector<string> > & geno, int index); 96 double unphred(map< string, vector<string> > & geno, int index); 103 double unphred(map< string, vector<string> > & geno, int index); 111 double unphred(map< string, vector<string> > & geno, int index);
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H A D | var.cpp | 112 double gt::unphred(map< string, vector<string> > & geno, int index){ in unphred() argument 116 double gl::unphred(map< string, vector<string> > & geno, int index){ in unphred() argument 118 double unphreded = atof(geno["GL"][index].c_str()); in unphred() 122 double gp::unphred(map< string, vector<string> > & geno, int index){ in unphred() argument 124 double unphreded = atof(geno["GP"][index].c_str()); in unphred() 128 double pl::unphred(map< string, vector<string> > & geno, int index){ in unphred() argument 130 double unphreded = atof(geno["PL"][index].c_str()); in unphred()
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/dports/biology/gemma/GEMMA-0.98.3/doc/example/ |
H A D | data-munging.org | 73 bio-table --skip 20 BXD.geno > BXD_noheader.geno 94 bio-table --rewrite 'field[0] = "X\tY\t" + field[0]' BXD_cols.geno > BXD_cols2.geno 151 gemma -g BXD_mine.geno -p BXD_pheno.csv -gk 160 gemma -g BXD_mine.geno -p BXD_pheno.csv -gk -debug 187 gemma -g BXD_mine.geno -p BXD_pheno.csv -gk -n 2 205 gemma -g BXD_mine.geno \ 224 -g BXD_mine.geno \ 238 -g BXD_mine.geno \ 260 -g BXD_mine.geno \ 272 -g BXD_mine.geno \ [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/snp_store/tests/ |
H A D | indels_realign_m0mp1oa.gff | 1 …. ID=6882;size=-1;count=33;seq=A;depth=34;quality=38;homorun=9;bsi;seqContext=CAACAAAAAAAA;geno=hom 2 …. ID=8883;size=-1;count=10;seq=C;depth=21;quality=19;homorun=3;bsi;seqContext=AACAAAGACACA;geno=het 3 … 8963 1 + . ID=8963;size=1;count=23;depth=23;quality=20;homorun=3;seqContext=TAAGAGAAAGCAG;geno=hom
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H A D | indels_realign.gff | 1 …. ID=6881;size=-1;count=35;seq=A;depth=37;quality=24;homorun=9;bsi;seqContext=ACAACAAAAAAA;geno=hom 2 …ID=8883;size=-5;count=3;seq=GACAC;depth=11;quality=8;homorun=3;bsi;seqContext=AACAAAGACACA;geno=het 3 …3 1 + . ID=8963;size=1;count=21;depth=21;quality=28;homorun=3;bsi;seqContext=TAAGAGAAAGCAG;geno=hom
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H A D | indels_realign_m0mp1oa_it1ipt01.gff | 1 …. ID=6881;size=-1;count=36;seq=A;depth=38;quality=24;homorun=9;bsi;seqContext=ACAACAAAAAAA;geno=hom 2 …ID=8883;size=-5;count=3;seq=GACAC;depth=12;quality=8;homorun=3;bsi;seqContext=AACAAAGACACA;geno=het 3 …3 1 + . ID=8963;size=1;count=21;depth=21;quality=28;homorun=3;bsi;seqContext=TAAGAGAAAGCAG;geno=hom
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H A D | indels_realign_m1mp1oa.gff | 1 …. ID=6881;size=-1;count=36;seq=A;depth=38;quality=24;homorun=9;bsi;seqContext=ACAACAAAAAAA;geno=hom 2 …ID=8883;size=-5;count=3;seq=GACAC;depth=12;quality=8;homorun=3;bsi;seqContext=AACAAAGACACA;geno=het 3 …3 1 + . ID=8963;size=1;count=21;depth=21;quality=28;homorun=3;bsi;seqContext=TAAGAGAAAGCAG;geno=hom
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H A D | indels_default.gff | 1 …n 6879 6879 0.529412 + . ID=6880;size=-1;count=18;seq=A;ebiDepth=34;depth=34;homorun=9;bsi;geno=het 2 …gff deletion 8963 8963 0.913043 + . ID=8963;size=1;count=21;ebiDepth=23;depth=23;homorun=3;geno=hom
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/dports/biology/plink/plink-ng-79b2df8c/2.0/Tests/TEST_MAF_FILTER/ |
H A D | run_tests.sh | 6 plink --bfile tmp_data --keep-allele-order --geno 0.1 --maf 0.01 --make-bed --out plink_filtered 8 $1/plink2 $2 $3 --bfile tmp_data --geno 0.1 --maf 0.01 --make-bpgen --out new_filtered 12 $1/plink2 $2 $3 --bpfile tmp_data --geno 0.1 --maf 0.01 --make-bpgen --out new_filtered2
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/dports/biology/gemma/GEMMA-0.98.3/test/performance/ |
H A D | releases.org | 20 time ./bin/gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -a ./exa… 22 time ./bin/gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -n 1 -a … 24 time ./bin/gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -n 1 2 -… 96 time ./bin/gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -a ./exa… 113 time ./bin/gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -n 1 -a … 184 time ./bin/gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -a ./exa… 202 time ./gemma-0.98.1-linux-static -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.ph… 257 time ./bin/gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -a ./exa… 275 time ./bin/gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -n 1 -a … 297 time ./bin/gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -n 1 2 -… [all …]
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/dports/biology/vcftools/vcftools-0.1.16/src/cpp/ |
H A D | variant_file_output.cpp | 475 if ((geno.first == aa_idx) && (geno.second == aa_idx)) in output_indv_burden() 477 else if ((geno.first >= 0) && (geno.second >= 0) && (geno.first != geno.second)) in output_indv_burden() 479 else if ((geno.first >= 0) && (geno.second >= 0) && (geno.first == geno.second)) in output_indv_burden() 603 if ((geno.first != aa_idx) && (geno.first >= 0)) in output_indv_freq_burden() 605 if ((double_count_hom_alt == 0) || (geno.first != geno.second)) in output_indv_freq_burden() 607 if ((geno.second != aa_idx) && (geno.second >= 0)) in output_indv_freq_burden() 1361 geno.first = -1; geno.second = -1; in output_haplotype_count() 1787 pair<int,int> geno; in output_genotype_chisq() local 1954 pair<int,int> geno; in output_interchromosomal_genotype_r2() local 2771 if ((geno.first == a) || (geno.second == a)) in output_singletons() [all …]
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