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Searched refs:bcf_p1aux_t (Results 1 – 17 of 17) sorted by relevance

/dports/biology/seqan1/seqan-1.3.1/lib/samtools/bcftools/
H A Dprob1.h7 typedef struct __bcf_p1aux_t bcf_p1aux_t; typedef
25 bcf_p1aux_t *bcf_p1_init(int n);
26 void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta);
27 void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta);
28 void bcf_p1_destroy(bcf_p1aux_t *ma);
29 int bcf_p1_cal(bcf1_t *b, bcf_p1aux_t *ma, bcf_p1rst_t *rst);
30 int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k);
31 void bcf_p1_dump_afs(bcf_p1aux_t *ma);
32 int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn);
33 long double bcf_p1_cal_g3(bcf_p1aux_t *p1a, double g[3]);
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H A Dprob1.c53 void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x) in bcf_p1_indel_prior()
133 bcf_p1aux_t *bcf_p1_init(int n) in bcf_p1_init()
135 bcf_p1aux_t *ma; in bcf_p1_init()
137 ma = calloc(1, sizeof(bcf_p1aux_t)); in bcf_p1_init()
158 int bcf_p1_set_n1(bcf_p1aux_t *b, int n1) in bcf_p1_set_n1()
165 void bcf_p1_set_folded(bcf_p1aux_t *p1a) in bcf_p1_set_folded()
174 void bcf_p1_destroy(bcf_p1aux_t *ma) in bcf_p1_destroy()
245 static void mc_cal_y_core(bcf_p1aux_t *ma, int beg) in mc_cal_y_core()
289 static void mc_cal_y(bcf_p1aux_t *ma) in mc_cal_y()
329 static double mc_cal_afs(bcf_p1aux_t *ma) in mc_cal_afs()
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H A Dcall1.c150 static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double … in update_bcf1()
205 extern void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x); in bcfview()
211 bcf_p1aux_t *p1 = 0; in bcfview()
/dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/bcftools/
H A Dprob1.h7 typedef struct __bcf_p1aux_t bcf_p1aux_t; typedef
25 bcf_p1aux_t *bcf_p1_init(int n, uint8_t *ploidy);
26 void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta);
27 void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta);
28 void bcf_p1_destroy(bcf_p1aux_t *ma);
29 int bcf_p1_cal(const bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst);
30 int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k);
31 void bcf_p1_dump_afs(bcf_p1aux_t *ma);
32 int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn);
33 int bcf_p1_set_n1(bcf_p1aux_t *b, int n1);
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H A Dprob1.c53 void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x) in bcf_p1_indel_prior()
91 int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn) in bcf_p1_read_prior()
133 bcf_p1aux_t *bcf_p1_init(int n, uint8_t *ploidy) in bcf_p1_init()
135 bcf_p1aux_t *ma; in bcf_p1_init()
137 ma = calloc(1, sizeof(bcf_p1aux_t)); in bcf_p1_init()
169 int bcf_p1_set_n1(bcf_p1aux_t *b, int n1) in bcf_p1_set_n1()
180 void bcf_p1_destroy(bcf_p1aux_t *ma) in bcf_p1_destroy()
197 static int cal_pdg(const bcf1_t *b, bcf_p1aux_t *ma) in cal_pdg()
245 static void mc_cal_y_core(bcf_p1aux_t *ma, int beg) in mc_cal_y_core()
330 static void mc_cal_y(bcf_p1aux_t *ma) in mc_cal_y()
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H A Dcall1.c134 static int update_bcf1(bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int fl… in update_bcf1()
319 extern void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x); in bcfview()
333 bcf_p1aux_t *p1 = 0; in bcfview()
/dports/biology/bcftools/bcftools-1.14/
H A Dprob1.h51 } bcf_p1aux_t; typedef
75 bcf_p1aux_t *bcf_p1_init(int n_smpl, uint8_t *ploidy);
76 void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta);
77 void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta);
78 void bcf_p1_destroy(bcf_p1aux_t *ma);
79 void bcf_p1_set_ploidy(bcf1_t *b, bcf_p1aux_t *ma);
81 int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k, int is_var);
82 void bcf_p1_dump_afs(bcf_p1aux_t *ma);
83 int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn);
84 int bcf_p1_set_n1(bcf_p1aux_t *b, int n1);
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H A Dprob1.c46 void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x) in bcf_p1_indel_prior()
86 bcf_p1aux_t *bcf_p1_init(int n_smpl, uint8_t *ploidy) in bcf_p1_init()
88 bcf_p1aux_t *ma; in bcf_p1_init()
90 ma = (bcf_p1aux_t*) calloc(1, sizeof(bcf_p1aux_t)); in bcf_p1_init()
123 int bcf_p1_get_M(bcf_p1aux_t *b) { return b->M; } in bcf_p1_get_M()
125 int bcf_p1_set_n1(bcf_p1aux_t *b, int n1) in bcf_p1_set_n1()
136 void bcf_p1_destroy(bcf_p1aux_t *ma) in bcf_p1_destroy()
157 static int cal_pdg(const bcf1_t *b, bcf_p1aux_t *ma) in cal_pdg()
219 static void mc_cal_y_core(bcf_p1aux_t *ma, int beg) in mc_cal_y_core()
311 static void mc_cal_y(bcf_p1aux_t *ma) in mc_cal_y()
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H A Dccall.c38 bcf_p1aux_t *p1;
178 bcf_p1aux_t *p1 = call->cdat->p1; in update_bcf1()
/dports/biology/bio-mocha/bcftools-1.14/
H A Dprob1.h51 } bcf_p1aux_t; typedef
75 bcf_p1aux_t *bcf_p1_init(int n_smpl, uint8_t *ploidy);
76 void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta);
77 void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta);
78 void bcf_p1_destroy(bcf_p1aux_t *ma);
79 void bcf_p1_set_ploidy(bcf1_t *b, bcf_p1aux_t *ma);
81 int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k, int is_var);
82 void bcf_p1_dump_afs(bcf_p1aux_t *ma);
83 int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn);
84 int bcf_p1_set_n1(bcf_p1aux_t *b, int n1);
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H A Dprob1.c46 void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x) in bcf_p1_indel_prior()
86 bcf_p1aux_t *bcf_p1_init(int n_smpl, uint8_t *ploidy) in bcf_p1_init()
88 bcf_p1aux_t *ma; in bcf_p1_init()
90 ma = (bcf_p1aux_t*) calloc(1, sizeof(bcf_p1aux_t)); in bcf_p1_init()
123 int bcf_p1_get_M(bcf_p1aux_t *b) { return b->M; } in bcf_p1_get_M()
125 int bcf_p1_set_n1(bcf_p1aux_t *b, int n1) in bcf_p1_set_n1()
136 void bcf_p1_destroy(bcf_p1aux_t *ma) in bcf_p1_destroy()
157 static int cal_pdg(const bcf1_t *b, bcf_p1aux_t *ma) in cal_pdg()
219 static void mc_cal_y_core(bcf_p1aux_t *ma, int beg) in mc_cal_y_core()
311 static void mc_cal_y(bcf_p1aux_t *ma) in mc_cal_y()
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H A Dccall.c38 bcf_p1aux_t *p1;
178 bcf_p1aux_t *p1 = call->cdat->p1; in update_bcf1()
/dports/biology/py-pysam/pysam-0.18.0/bcftools/
H A Dprob1.h51 } bcf_p1aux_t; typedef
75 bcf_p1aux_t *bcf_p1_init(int n_smpl, uint8_t *ploidy);
76 void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta);
77 void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta);
78 void bcf_p1_destroy(bcf_p1aux_t *ma);
79 void bcf_p1_set_ploidy(bcf1_t *b, bcf_p1aux_t *ma);
81 int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k, int is_var);
82 void bcf_p1_dump_afs(bcf_p1aux_t *ma);
83 int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn);
84 int bcf_p1_set_n1(bcf_p1aux_t *b, int n1);
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H A Dprob1.c46 void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x) in bcf_p1_indel_prior()
86 bcf_p1aux_t *bcf_p1_init(int n_smpl, uint8_t *ploidy) in bcf_p1_init()
88 bcf_p1aux_t *ma; in bcf_p1_init()
90 ma = (bcf_p1aux_t*) calloc(1, sizeof(bcf_p1aux_t)); in bcf_p1_init()
123 int bcf_p1_get_M(bcf_p1aux_t *b) { return b->M; } in bcf_p1_get_M()
125 int bcf_p1_set_n1(bcf_p1aux_t *b, int n1) in bcf_p1_set_n1()
136 void bcf_p1_destroy(bcf_p1aux_t *ma) in bcf_p1_destroy()
157 static int cal_pdg(const bcf1_t *b, bcf_p1aux_t *ma) in cal_pdg()
219 static void mc_cal_y_core(bcf_p1aux_t *ma, int beg) in mc_cal_y_core()
311 static void mc_cal_y(bcf_p1aux_t *ma) in mc_cal_y()
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H A Dprob1.c.pysam.c48 void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x) in bcf_p1_indel_prior()
88 bcf_p1aux_t *bcf_p1_init(int n_smpl, uint8_t *ploidy) in bcf_p1_init()
90 bcf_p1aux_t *ma; in bcf_p1_init()
92 ma = (bcf_p1aux_t*) calloc(1, sizeof(bcf_p1aux_t)); in bcf_p1_init()
125 int bcf_p1_get_M(bcf_p1aux_t *b) { return b->M; } in bcf_p1_get_M()
127 int bcf_p1_set_n1(bcf_p1aux_t *b, int n1) in bcf_p1_set_n1()
138 void bcf_p1_destroy(bcf_p1aux_t *ma) in bcf_p1_destroy()
159 static int cal_pdg(const bcf1_t *b, bcf_p1aux_t *ma) in cal_pdg()
221 static void mc_cal_y_core(bcf_p1aux_t *ma, int beg) in mc_cal_y_core()
313 static void mc_cal_y(bcf_p1aux_t *ma) in mc_cal_y()
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H A Dccall.c38 bcf_p1aux_t *p1;
178 bcf_p1aux_t *p1 = call->cdat->p1; in update_bcf1()
H A Dccall.c.pysam.c40 bcf_p1aux_t *p1;
180 bcf_p1aux_t *p1 = call->cdat->p1; in update_bcf1()