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/dports/biology/mapm3/mapm3-3.0_1/quant/
H A Dqlow.h30 #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++)
H A Dqdata.c142 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];
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H A Dqctm.c401 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];
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/dports/biology/vt/vt-0.57721/
H A Dprofile_chm1.cpp79 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()
H A Dprofile_na12878.cpp84 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()
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/dports/biology/bamutil/bamUtil-1.0.15/libStatGen/general/
H A DPedigree.cpp572 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()
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/dports/biology/gemma/GEMMA-0.98.3/src/
H A Dgemma_io.cpp757 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()
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H A Dvarcov.cpp266 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()
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H A Dprdt.cpp220 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()
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/dports/biology/gemma/GEMMA-0.98.3/test/
H A Dtest_suite.sh9 $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 \
/dports/biology/vcflib/vcflib-1.0.2/src/
H A Dvar.hpp66 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);
H A Dvar.cpp130 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()
/dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/
H A Dvar.hpp57 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);
H A Dvar.cpp112 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()
/dports/biology/freebayes/freebayes-1.3.5/vcflib/src/
H A Dvar.hpp57 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);
H A Dvar.cpp112 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()
/dports/biology/gemma/GEMMA-0.98.3/doc/example/
H A Ddata-munging.org73 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 \
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/snp_store/tests/
H A Dindels_realign_m0mp1oa.gff1 …. 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
H A Dindels_realign.gff1 …. 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
H A Dindels_realign_m0mp1oa_it1ipt01.gff1 …. 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
H A Dindels_realign_m1mp1oa.gff1 …. 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
H A Dindels_default.gff1 …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
/dports/biology/plink/plink-ng-79b2df8c/2.0/Tests/TEST_MAF_FILTER/
H A Drun_tests.sh6 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
/dports/biology/gemma/GEMMA-0.98.3/test/performance/
H A Dreleases.org20 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 …]
/dports/biology/vcftools/vcftools-0.1.16/src/cpp/
H A Dvariant_file_output.cpp475 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()
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