/dports/biology/seqan1/seqan-1.3.1/lib/samtools/bcftools/ |
H A D | prob1.h | 7 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]); [all …]
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H A D | prob1.c | 53 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() [all …]
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H A D | call1.c | 150 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()
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/dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/bcftools/ |
H A D | prob1.h | 7 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); [all …]
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H A D | prob1.c | 53 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() [all …]
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H A D | call1.c | 134 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()
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/dports/biology/bcftools/bcftools-1.14/ |
H A D | prob1.h | 51 } 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); [all …]
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H A D | prob1.c | 46 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() [all …]
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H A D | ccall.c | 38 bcf_p1aux_t *p1; 178 bcf_p1aux_t *p1 = call->cdat->p1; in update_bcf1()
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/dports/biology/bio-mocha/bcftools-1.14/ |
H A D | prob1.h | 51 } 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); [all …]
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H A D | prob1.c | 46 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() [all …]
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H A D | ccall.c | 38 bcf_p1aux_t *p1; 178 bcf_p1aux_t *p1 = call->cdat->p1; in update_bcf1()
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/dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
H A D | prob1.h | 51 } 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); [all …]
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H A D | prob1.c | 46 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() [all …]
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H A D | prob1.c.pysam.c | 48 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() [all …]
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H A D | ccall.c | 38 bcf_p1aux_t *p1; 178 bcf_p1aux_t *p1 = call->cdat->p1; in update_bcf1()
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H A D | ccall.c.pysam.c | 40 bcf_p1aux_t *p1; 180 bcf_p1aux_t *p1 = call->cdat->p1; in update_bcf1()
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