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/dports/biology/bcftools/bcftools-1.14/
H A Dbam2bcf.c50 bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100; in bcf_call_init()
80 free(bca->ref_pos); free(bca->alt_pos); in bcf_call_destroy()
81 free(bca->iref_pos); free(bca->ialt_pos); in bcf_call_destroy()
84 free(bca->ref_mq); free(bca->alt_mq); in bcf_call_destroy()
85 free(bca->iref_mq); free(bca->ialt_mq); in bcf_call_destroy()
86 free(bca->ref_bq); free(bca->alt_bq); in bcf_call_destroy()
87 free(bca->fwd_mqs); free(bca->rev_mqs); in bcf_call_destroy()
89 free(bca->bases); free(bca->inscns); free(bca); in bcf_call_destroy()
146 memset(bca->ref_pos,0,sizeof(int)*bca->npos); in bcf_callaux_clean()
147 memset(bca->alt_pos,0,sizeof(int)*bca->npos); in bcf_callaux_clean()
[all …]
H A Dbam2bcf_indel.c82 q = bca->openQ + bca->extQ * (abs(l) - 1); in est_seqQ()
174 bca->max_support = bca->max_frac = 0; in bcf_cgp_find_types()
203 bca->max_support = na, bca->max_frac = frac; in bcf_cgp_find_types()
215 if ( !bca->per_sample_flt ) in bcf_cgp_find_types()
640 bca->maxins = max_ins; in bcf_cgp_compute_indelQ()
641 bca->inscns = (char*) realloc(bca->inscns, bca->maxins * 4); in bcf_cgp_compute_indelQ()
642 if (bca->maxins && !bca->inscns) in bcf_cgp_compute_indelQ()
659 if (bca->maxins) in bcf_cgp_compute_indelQ()
660 memcpy(&bca->inscns[t * bca->maxins], in bcf_cgp_compute_indelQ()
722 left = pos > bca->indel_win_size ? pos - bca->indel_win_size : 0; in bcf_call_gap_prep()
[all …]
/dports/biology/bio-mocha/bcftools-1.14/
H A Dbam2bcf.c50 bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100; in bcf_call_init()
80 free(bca->ref_pos); free(bca->alt_pos); in bcf_call_destroy()
81 free(bca->iref_pos); free(bca->ialt_pos); in bcf_call_destroy()
84 free(bca->ref_mq); free(bca->alt_mq); in bcf_call_destroy()
85 free(bca->iref_mq); free(bca->ialt_mq); in bcf_call_destroy()
86 free(bca->ref_bq); free(bca->alt_bq); in bcf_call_destroy()
87 free(bca->fwd_mqs); free(bca->rev_mqs); in bcf_call_destroy()
89 free(bca->bases); free(bca->inscns); free(bca); in bcf_call_destroy()
146 memset(bca->ref_pos,0,sizeof(int)*bca->npos); in bcf_callaux_clean()
147 memset(bca->alt_pos,0,sizeof(int)*bca->npos); in bcf_callaux_clean()
[all …]
H A Dbam2bcf_indel.c82 q = bca->openQ + bca->extQ * (abs(l) - 1); in est_seqQ()
174 bca->max_support = bca->max_frac = 0; in bcf_cgp_find_types()
203 bca->max_support = na, bca->max_frac = frac; in bcf_cgp_find_types()
215 if ( !bca->per_sample_flt ) in bcf_cgp_find_types()
640 bca->maxins = max_ins; in bcf_cgp_compute_indelQ()
641 bca->inscns = (char*) realloc(bca->inscns, bca->maxins * 4); in bcf_cgp_compute_indelQ()
642 if (bca->maxins && !bca->inscns) in bcf_cgp_compute_indelQ()
659 if (bca->maxins) in bcf_cgp_compute_indelQ()
660 memcpy(&bca->inscns[t * bca->maxins], in bcf_cgp_compute_indelQ()
722 left = pos > bca->indel_win_size ? pos - bca->indel_win_size : 0; in bcf_call_gap_prep()
[all …]
/dports/biology/py-pysam/pysam-0.18.0/bcftools/
H A Dbam2bcf.c50 bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100; in bcf_call_init()
80 free(bca->ref_pos); free(bca->alt_pos); in bcf_call_destroy()
81 free(bca->iref_pos); free(bca->ialt_pos); in bcf_call_destroy()
84 free(bca->ref_mq); free(bca->alt_mq); in bcf_call_destroy()
85 free(bca->iref_mq); free(bca->ialt_mq); in bcf_call_destroy()
86 free(bca->ref_bq); free(bca->alt_bq); in bcf_call_destroy()
87 free(bca->fwd_mqs); free(bca->rev_mqs); in bcf_call_destroy()
89 free(bca->bases); free(bca->inscns); free(bca); in bcf_call_destroy()
146 memset(bca->ref_pos,0,sizeof(int)*bca->npos); in bcf_callaux_clean()
147 memset(bca->alt_pos,0,sizeof(int)*bca->npos); in bcf_callaux_clean()
[all …]
H A Dbam2bcf.c.pysam.c52 bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100; in bcf_call_init()
82 free(bca->ref_pos); free(bca->alt_pos); in bcf_call_destroy()
83 free(bca->iref_pos); free(bca->ialt_pos); in bcf_call_destroy()
86 free(bca->ref_mq); free(bca->alt_mq); in bcf_call_destroy()
87 free(bca->iref_mq); free(bca->ialt_mq); in bcf_call_destroy()
88 free(bca->ref_bq); free(bca->alt_bq); in bcf_call_destroy()
89 free(bca->fwd_mqs); free(bca->rev_mqs); in bcf_call_destroy()
91 free(bca->bases); free(bca->inscns); free(bca); in bcf_call_destroy()
148 memset(bca->ref_pos,0,sizeof(int)*bca->npos); in bcf_callaux_clean()
149 memset(bca->alt_pos,0,sizeof(int)*bca->npos); in bcf_callaux_clean()
[all …]
H A Dbam2bcf_indel.c82 q = bca->openQ + bca->extQ * (abs(l) - 1); in est_seqQ()
174 bca->max_support = bca->max_frac = 0; in bcf_cgp_find_types()
203 bca->max_support = na, bca->max_frac = frac; in bcf_cgp_find_types()
215 if ( !bca->per_sample_flt ) in bcf_cgp_find_types()
640 bca->maxins = max_ins; in bcf_cgp_compute_indelQ()
641 bca->inscns = (char*) realloc(bca->inscns, bca->maxins * 4); in bcf_cgp_compute_indelQ()
642 if (bca->maxins && !bca->inscns) in bcf_cgp_compute_indelQ()
659 if (bca->maxins) in bcf_cgp_compute_indelQ()
660 memcpy(&bca->inscns[t * bca->maxins], in bcf_cgp_compute_indelQ()
722 left = pos > bca->indel_win_size ? pos - bca->indel_win_size : 0; in bcf_call_gap_prep()
[all …]
H A Dbam2bcf_indel.c.pysam.c84 q = bca->openQ + bca->extQ * (abs(l) - 1); in est_seqQ()
176 bca->max_support = bca->max_frac = 0; in bcf_cgp_find_types()
205 bca->max_support = na, bca->max_frac = frac; in bcf_cgp_find_types()
217 if ( !bca->per_sample_flt ) in bcf_cgp_find_types()
642 bca->maxins = max_ins; in bcf_cgp_compute_indelQ()
643 bca->inscns = (char*) realloc(bca->inscns, bca->maxins * 4); in bcf_cgp_compute_indelQ()
644 if (bca->maxins && !bca->inscns) in bcf_cgp_compute_indelQ()
661 if (bca->maxins) in bcf_cgp_compute_indelQ()
662 memcpy(&bca->inscns[t * bca->maxins], in bcf_cgp_compute_indelQ()
724 left = pos > bca->indel_win_size ? pos - bca->indel_win_size : 0; in bcf_call_gap_prep()
[all …]
/dports/biology/py-pysam/pysam-0.18.0/samtools/
H A Dbam2bcf.c51 bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100; in bcf_call_init()
58 bca->ref_pos = malloc(bca->npos*sizeof(int)); in bcf_call_init()
74 if (bca->npos) { free(bca->ref_pos); free(bca->alt_pos); bca->npos = 0; } in bcf_call_destroy()
75 free(bca->ref_mq); free(bca->alt_mq); free(bca->ref_bq); free(bca->alt_bq); in bcf_call_destroy()
76 free(bca->fwd_mqs); free(bca->rev_mqs); in bcf_call_destroy()
78 free(bca->bases); free(bca->inscns); free(bca); in bcf_call_destroy()
167 bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases); in bcf_call_glfgen()
660 call->mwu_pos = calc_mwu_bias(bca->ref_pos, bca->alt_pos, bca->npos); in bcf_call_combine()
661 call->mwu_mq = calc_mwu_bias(bca->ref_mq, bca->alt_mq, bca->nqual); in bcf_call_combine()
662 call->mwu_bq = calc_mwu_bias(bca->ref_bq, bca->alt_bq, bca->nqual); in bcf_call_combine()
[all …]
H A Dbam2bcf.c.pysam.c53 bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100; in bcf_call_init()
60 bca->ref_pos = malloc(bca->npos*sizeof(int)); in bcf_call_init()
76 if (bca->npos) { free(bca->ref_pos); free(bca->alt_pos); bca->npos = 0; } in bcf_call_destroy()
77 free(bca->ref_mq); free(bca->alt_mq); free(bca->ref_bq); free(bca->alt_bq); in bcf_call_destroy()
78 free(bca->fwd_mqs); free(bca->rev_mqs); in bcf_call_destroy()
80 free(bca->bases); free(bca->inscns); free(bca); in bcf_call_destroy()
169 bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases); in bcf_call_glfgen()
662 call->mwu_pos = calc_mwu_bias(bca->ref_pos, bca->alt_pos, bca->npos); in bcf_call_combine()
663 call->mwu_mq = calc_mwu_bias(bca->ref_mq, bca->alt_mq, bca->nqual); in bcf_call_combine()
664 call->mwu_bq = calc_mwu_bias(bca->ref_bq, bca->alt_bq, bca->nqual); in bcf_call_combine()
[all …]
/dports/biology/samtools/samtools-1.14/
H A Dbam2bcf.c51 bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100; in bcf_call_init()
58 bca->ref_pos = malloc(bca->npos*sizeof(int)); in bcf_call_init()
74 if (bca->npos) { free(bca->ref_pos); free(bca->alt_pos); bca->npos = 0; } in bcf_call_destroy()
75 free(bca->ref_mq); free(bca->alt_mq); free(bca->ref_bq); free(bca->alt_bq); in bcf_call_destroy()
76 free(bca->fwd_mqs); free(bca->rev_mqs); in bcf_call_destroy()
78 free(bca->bases); free(bca->inscns); free(bca); in bcf_call_destroy()
167 bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases); in bcf_call_glfgen()
660 call->mwu_pos = calc_mwu_bias(bca->ref_pos, bca->alt_pos, bca->npos); in bcf_call_combine()
661 call->mwu_mq = calc_mwu_bias(bca->ref_mq, bca->alt_mq, bca->nqual); in bcf_call_combine()
662 call->mwu_bq = calc_mwu_bias(bca->ref_bq, bca->alt_bq, bca->nqual); in bcf_call_combine()
[all …]
/dports/biology/seqan1/seqan-1.3.1/lib/samtools/
H A Dbam2bcf.c19 bcf_callaux_t *bca; in bcf_call_init() local
22 bca->capQ = 60; in bcf_call_init()
23 bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100; in bcf_call_init()
26 return bca; in bcf_call_init()
31 if (bca == 0) return; in bcf_call_destroy()
33 free(bca->bases); free(bca->inscns); free(bca); in bcf_call_destroy()
50 bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases); in bcf_call_glfgen()
64 mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ; in bcf_call_glfgen()
92 errmod_cal(bca->e, n, 5, bca->bases, r->p); in bcf_call_glfgen()
195 for (j = -bca->indel_types[bc->a[i]]; j < bca->indelreg; ++j) in bcf_call2bcf()
[all …]
/dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/
H A Dbam2bcf.c20 bcf_callaux_t *bca; in bcf_call_init() local
23 bca->capQ = 60; in bcf_call_init()
24 bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100; in bcf_call_init()
28 bca->min_support = 1; in bcf_call_init()
29 return bca; in bcf_call_init()
34 if (bca == 0) return; in bcf_call_destroy()
36 free(bca->bases); free(bca->inscns); free(bca); in bcf_call_destroy()
54 bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases); in bcf_call_glfgen()
69 mapQ = mapQ < bca->capQ? mapQ : bca->capQ; in bcf_call_glfgen()
97 errmod_cal(bca->e, n, 5, bca->bases, r->p); in bcf_call_glfgen()
[all …]
/dports/devel/hs-spago/spago-0.20.3/_cabal_deps/kan-extensions-5.2.2/src/Data/Functor/Invariant/
H A DDay.hs38 invmap f g (Day fb gc bca abc) = Day fb gc ((f .) . bca) (abc . g)
53 assoc (Day fb (Day gd he dec cde) bca abc) = flip (Day (Day fb gd (,) id) he) f g
60 bca b (dec d e)
71 disassoc (Day (Day fb gc deb bde) hd bca abc) = Day fb (Day gc hd (,) id) f g
74 bca (deb e d) c
86 swapped (Day fb gc bca abc) = Day gc fb (flip bca) (\a -> let (b, c) = abc a in (c, b))
113 elim1 (Day (Identity b) fc bca abc) = invmap (bca b) (snd . abc) fc
122 elim2 (Day fb (Identity c) bca abc) = invmap (flip bca c) (fst . abc) fb
132 trans1 fg (Day fb hc bca abc) = Day (fg fb) hc bca abc
142 trans2 gh (Day fb gc bca abc) = Day fb (gh gc) bca abc
[all …]
/dports/devel/hs-haskell-language-server/haskell-language-server-1.4.0/_cabal_deps/kan-extensions-5.2.2/src/Data/Functor/Invariant/
H A DDay.hs38 invmap f g (Day fb gc bca abc) = Day fb gc ((f .) . bca) (abc . g)
53 assoc (Day fb (Day gd he dec cde) bca abc) = flip (Day (Day fb gd (,) id) he) f g
60 bca b (dec d e)
71 disassoc (Day (Day fb gc deb bde) hd bca abc) = Day fb (Day gc hd (,) id) f g
74 bca (deb e d) c
86 swapped (Day fb gc bca abc) = Day gc fb (flip bca) (\a -> let (b, c) = abc a in (c, b))
113 elim1 (Day (Identity b) fc bca abc) = invmap (bca b) (snd . abc) fc
122 elim2 (Day fb (Identity c) bca abc) = invmap (flip bca c) (fst . abc) fb
132 trans1 fg (Day fb hc bca abc) = Day (fg fb) hc bca abc
142 trans2 gh (Day fb gc bca abc) = Day fb (gh gc) bca abc
[all …]
/dports/security/hs-cryptol/cryptol-2.11.0/_cabal_deps/kan-extensions-5.2.2/src/Data/Functor/Invariant/
H A DDay.hs38 invmap f g (Day fb gc bca abc) = Day fb gc ((f .) . bca) (abc . g)
53 assoc (Day fb (Day gd he dec cde) bca abc) = flip (Day (Day fb gd (,) id) he) f g
60 bca b (dec d e)
71 disassoc (Day (Day fb gc deb bde) hd bca abc) = Day fb (Day gc hd (,) id) f g
74 bca (deb e d) c
86 swapped (Day fb gc bca abc) = Day gc fb (flip bca) (\a -> let (b, c) = abc a in (c, b))
113 elim1 (Day (Identity b) fc bca abc) = invmap (bca b) (snd . abc) fc
122 elim2 (Day fb (Identity c) bca abc) = invmap (flip bca c) (fst . abc) fb
132 trans1 fg (Day fb hc bca abc) = Day (fg fb) hc bca abc
142 trans2 gh (Day fb gc bca abc) = Day fb (gh gc) bca abc
[all …]
/dports/www/hs-DAV/DAV-1.3.4/_cabal_deps/kan-extensions-5.2/src/Data/Functor/Invariant/
H A DDay.hs38 invmap f g (Day fb gc bca abc) = Day fb gc ((f .) . bca) (abc . g)
53 assoc (Day fb (Day gd he dec cde) bca abc) = flip (Day (Day fb gd (,) id) he) f g
60 bca b (dec d e)
71 disassoc (Day (Day fb gc deb bde) hd bca abc) = Day fb (Day gc hd (,) id) f g
74 bca (deb e d) c
86 swapped (Day fb gc bca abc) = Day gc fb (flip bca) (\a -> let (b, c) = abc a in (c, b))
113 elim1 (Day (Identity b) fc bca abc) = invmap (bca b) (snd . abc) fc
122 elim2 (Day fb (Identity c) bca abc) = invmap (flip bca c) (fst . abc) fb
132 trans1 fg (Day fb hc bca abc) = Day (fg fb) hc bca abc
142 trans2 gh (Day fb gc bca abc) = Day fb (gh gc) bca abc
[all …]
/dports/www/hs-postgrest/postgrest-8.0.0/_cabal_deps/kan-extensions-5.2.2/src/Data/Functor/Invariant/
H A DDay.hs38 invmap f g (Day fb gc bca abc) = Day fb gc ((f .) . bca) (abc . g)
53 assoc (Day fb (Day gd he dec cde) bca abc) = flip (Day (Day fb gd (,) id) he) f g
60 bca b (dec d e)
71 disassoc (Day (Day fb gc deb bde) hd bca abc) = Day fb (Day gc hd (,) id) f g
74 bca (deb e d) c
86 swapped (Day fb gc bca abc) = Day gc fb (flip bca) (\a -> let (b, c) = abc a in (c, b))
113 elim1 (Day (Identity b) fc bca abc) = invmap (bca b) (snd . abc) fc
122 elim2 (Day fb (Identity c) bca abc) = invmap (flip bca c) (fst . abc) fb
132 trans1 fg (Day fb hc bca abc) = Day (fg fb) hc bca abc
142 trans2 gh (Day fb gc bca abc) = Day fb (gh gc) bca abc
[all …]
/dports/devel/hs-git-annex/git-annex-8.20210903/_cabal_deps/kan-extensions-5.2.3/src/Data/Functor/Invariant/
H A DDay.hs38 invmap f g (Day fb gc bca abc) = Day fb gc ((f .) . bca) (abc . g)
53 assoc (Day fb (Day gd he dec cde) bca abc) = flip (Day (Day fb gd (,) id) he) f g
60 bca b (dec d e)
71 disassoc (Day (Day fb gc deb bde) hd bca abc) = Day fb (Day gc hd (,) id) f g
74 bca (deb e d) c
86 swapped (Day fb gc bca abc) = Day gc fb (flip bca) (\a -> let (b, c) = abc a in (c, b))
113 elim1 (Day (Identity b) fc bca abc) = invmap (bca b) (snd . abc) fc
122 elim2 (Day fb (Identity c) bca abc) = invmap (flip bca c) (fst . abc) fb
132 trans1 fg (Day fb hc bca abc) = Day (fg fb) hc bca abc
142 trans2 gh (Day fb gc bca abc) = Day fb (gh gc) bca abc
[all …]
/dports/www/mod_php81/php-8.1.1/ext/standard/tests/strings/
H A Dsubstr_count_basic.phpt22 var_dump(substr_count($a, "bca"));
25 var_dump(substr_count($a, "bca"));
26 var_dump(substr_count($a, "bca", 200));
27 var_dump(substr_count($a, "bca", 200, null));
28 var_dump(substr_count($a, "bca", 200, 50));
29 var_dump(substr_count($a, "bca", -200));
30 var_dump(substr_count($a, "bca", -200, null));
31 var_dump(substr_count($a, "bca", -200, 50));
32 var_dump(substr_count($a, "bca", -200, -50));
/dports/lang/php81/php-8.1.1/ext/standard/tests/strings/
H A Dsubstr_count_basic.phpt22 var_dump(substr_count($a, "bca"));
25 var_dump(substr_count($a, "bca"));
26 var_dump(substr_count($a, "bca", 200));
27 var_dump(substr_count($a, "bca", 200, null));
28 var_dump(substr_count($a, "bca", 200, 50));
29 var_dump(substr_count($a, "bca", -200));
30 var_dump(substr_count($a, "bca", -200, null));
31 var_dump(substr_count($a, "bca", -200, 50));
32 var_dump(substr_count($a, "bca", -200, -50));
/dports/lang/php80/php-8.0.15/ext/standard/tests/strings/
H A Dsubstr_count_basic.phpt22 var_dump(substr_count($a, "bca"));
25 var_dump(substr_count($a, "bca"));
26 var_dump(substr_count($a, "bca", 200));
27 var_dump(substr_count($a, "bca", 200, null));
28 var_dump(substr_count($a, "bca", 200, 50));
29 var_dump(substr_count($a, "bca", -200));
30 var_dump(substr_count($a, "bca", -200, null));
31 var_dump(substr_count($a, "bca", -200, 50));
32 var_dump(substr_count($a, "bca", -200, -50));
/dports/www/mod_php80/php-8.0.15/ext/standard/tests/strings/
H A Dsubstr_count_basic.phpt22 var_dump(substr_count($a, "bca"));
25 var_dump(substr_count($a, "bca"));
26 var_dump(substr_count($a, "bca", 200));
27 var_dump(substr_count($a, "bca", 200, null));
28 var_dump(substr_count($a, "bca", 200, 50));
29 var_dump(substr_count($a, "bca", -200));
30 var_dump(substr_count($a, "bca", -200, null));
31 var_dump(substr_count($a, "bca", -200, 50));
32 var_dump(substr_count($a, "bca", -200, -50));
/dports/lang/php74/php-7.4.27/ext/standard/tests/strings/
H A Dsubstr_count_basic.phpt14 var_dump(@substr_count($a, "bca"));
17 var_dump(@substr_count($a, "bca"));
18 var_dump(substr_count($a, "bca", 200));
19 var_dump(substr_count($a, "bca", 200, 50));
20 var_dump(substr_count($a, "bca", -200));
21 var_dump(substr_count($a, "bca", -200, 50));
22 var_dump(substr_count($a, "bca", -200, -50));
/dports/lang/php73/php-7.3.33/ext/standard/tests/strings/
H A Dsubstr_count_basic.phpt14 var_dump(@substr_count($a, "bca"));
17 var_dump(@substr_count($a, "bca"));
18 var_dump(substr_count($a, "bca", 200));
19 var_dump(substr_count($a, "bca", 200, 50));
20 var_dump(substr_count($a, "bca", -200));
21 var_dump(substr_count($a, "bca", -200, 50));
22 var_dump(substr_count($a, "bca", -200, -50));

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