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- /* prob1.h -- mathematical utility functions.
-
- Copyright (C) 2010, 2011 Broad Institute.
- Copyright (C) 2012, 2013-2014 Genome Research Ltd.
-
- Author: Heng Li <lh3@sanger.ac.uk>
-
- Permission is hereby granted, free of charge, to any person obtaining a copy
- of this software and associated documentation files (the "Software"), to deal
- in the Software without restriction, including without limitation the rights
- to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- copies of the Software, and to permit persons to whom the Software is
- furnished to do so, subject to the following conditions:
-
- The above copyright notice and this permission notice shall be included in
- all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- THE SOFTWARE. */
-
- #ifndef BCF_PROB1_H
- #define BCF_PROB1_H
-
- #include <htslib/vcf.h>
- #include "call.h"
-
- typedef struct {
- int n; // Number of samples
- int M; // Total number of chromosomes across all samples (n*2 if all samples are diploid)
- int n1;
- int is_indel;
- uint8_t *ploidy; // haploid or diploid ONLY
- double *q2p, *pdg; // q2p maps from phread scaled to real likelihood, pdg -> P(D|g)
- double *phi; // Probability of seeing k reference alleles
- double *phi_indel;
- double *z, *zswap; // aux for afs
- double *z1, *z2, *phi1, *phi2; // only calculated when n1 is set
- double **hg; // hypergeometric distribution
- double *lf; // log factorial
- double t, t1, t2;
- double *afs, *afs1; // afs: accumulative allele frequency spectrum (AFS); afs1: site posterior distribution
- const int *PL; // point to PL
- int PL_len;
- int cons_llr; // pair and trio calling
- int64_t cons_gt;
- } bcf_p1aux_t;
-
- typedef struct {
- int rank0, perm_rank; // NB: perm_rank is always set to -1 by bcf_p1_cal()
- int ac; // ML alternative allele count
- double f_exp, f_flat, p_ref_folded, p_ref, p_var_folded, p_var;
- double cil, cih;
- double cmp[3], p_chi2, lrt; // used by contrast2()
- } bcf_p1rst_t;
-
- typedef struct {
- double p[4];
- double edb, mqb, bqb; // end distance bias, mapQ bias, baseQ bias
- int mq, depth, is_tested, d[4];
- } anno16_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_smpl, 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);
- void bcf_p1_set_ploidy(bcf1_t *b, bcf_p1aux_t *ma);
- int bcf_p1_cal(call_t *call, 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, int is_var);
- 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(call_t *call, const bcf1_t *b, int n1, int flag, double x[10]);
-
- #ifdef __cplusplus
- }
- #endif
-
- #endif
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