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comparison pyPRADA_1.2/tools/samtools-0.1.16/bam_maqcns.h @ 0:acc2ca1a3ba4

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author siyuan
date Thu, 20 Feb 2014 00:44:58 -0500
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1 #ifndef BAM_MAQCNS_H
2 #define BAM_MAQCNS_H
3
4 #include "glf.h"
5
6 #define BAM_ERRMOD_MAQ2 0
7 #define BAM_ERRMOD_MAQ 1
8 #define BAM_ERRMOD_SOAP 2
9
10 struct __bmc_aux_t;
11
12 typedef struct {
13 float het_rate, theta;
14 int n_hap, cap_mapQ, errmod, min_baseQ;
15
16 float eta, q_r;
17 double *fk, *coef;
18 double *lhet;
19 struct __bmc_aux_t *aux;
20 } bam_maqcns_t;
21
22 typedef struct {
23 int q_indel; // indel sequencing error, phred scaled
24 float r_indel; // indel prior
25 float r_snp; // snp prior
26 // hidden parameters, unchangeable from command line
27 int mm_penalty, indel_err, ambi_thres;
28 } bam_maqindel_opt_t;
29
30 typedef struct {
31 int indel1, indel2;
32 int cnt1, cnt2, cnt_anti;
33 int cnt_ref, cnt_ambi;
34 char *s[2];
35 //
36 int gt, gl[2];
37 int q_cns, q_ref;
38 } bam_maqindel_ret_t;
39
40 #ifdef __cplusplus
41 extern "C" {
42 #endif
43
44 bam_maqcns_t *bam_maqcns_init();
45 void bam_maqcns_prepare(bam_maqcns_t *bm);
46 void bam_maqcns_destroy(bam_maqcns_t *bm);
47 glf1_t *bam_maqcns_glfgen(int n, const bam_pileup1_t *pl, uint8_t ref_base, bam_maqcns_t *bm);
48 uint32_t bam_maqcns_call(int n, const bam_pileup1_t *pl, bam_maqcns_t *bm);
49 // return: cns<<28 | cns2<<24 | mapQ<<16 | cnsQ<<8 | cnsQ2
50 uint32_t glf2cns(const glf1_t *g, int q_r);
51
52 bam_maqindel_opt_t *bam_maqindel_opt_init();
53 bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, const bam_pileup1_t *pl, const char *ref,
54 int _n_types, int *_types);
55 void bam_maqindel_ret_destroy(bam_maqindel_ret_t*);
56
57 #ifdef __cplusplus
58 }
59 #endif
60
61 #endif