Mercurial > repos > siyuan > prada
diff pyPRADA_1.2/tools/samtools-0.1.16/bcftools/prob1.h @ 0:acc2ca1a3ba4
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author | siyuan |
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date | Thu, 20 Feb 2014 00:44:58 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pyPRADA_1.2/tools/samtools-0.1.16/bcftools/prob1.h Thu Feb 20 00:44:58 2014 -0500 @@ -0,0 +1,41 @@ +#ifndef BCF_PROB1_H +#define BCF_PROB1_H + +#include "bcf.h" + +struct __bcf_p1aux_t; +typedef struct __bcf_p1aux_t bcf_p1aux_t; + +typedef struct { + int rank0, perm_rank; // NB: perm_rank is always set to -1 by bcf_p1_cal() + double f_exp, f_flat, p_ref_folded, p_ref, p_var_folded, p_var; + double cil, cih; + double cmp[3], p_chi2; // used by contrast2() +} bcf_p1rst_t; + +#define MC_PTYPE_FULL 1 +#define MC_PTYPE_COND2 2 +#define MC_PTYPE_FLAT 3 + +#ifdef __cplusplus +extern "C" { +#endif + + bcf_p1aux_t *bcf_p1_init(int n, uint8_t *ploidy); + void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta); + void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta); + void bcf_p1_destroy(bcf_p1aux_t *ma); + int bcf_p1_cal(const bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst); + int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k); + void bcf_p1_dump_afs(bcf_p1aux_t *ma); + int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn); + int bcf_p1_set_n1(bcf_p1aux_t *b, int n1); + void bcf_p1_set_folded(bcf_p1aux_t *p1a); // only effective when set_n1() is not called + + int bcf_em1(const bcf1_t *b, int n1, int flag, double x[9]); + +#ifdef __cplusplus +} +#endif + +#endif