Mercurial > repos > ryanmorin > nextgen_variant_identification
comparison SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/bam_maqcns.h @ 0:74f5ea818cea
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author | ryanmorin |
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date | Wed, 12 Oct 2011 19:50:38 -0400 |
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-1:000000000000 | 0:74f5ea818cea |
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1 #ifndef BAM_MAQCNS_H | |
2 #define BAM_MAQCNS_H | |
3 | |
4 #include "glf.h" | |
5 | |
6 struct __bmc_aux_t; | |
7 | |
8 typedef struct { | |
9 float het_rate, theta; | |
10 int n_hap, cap_mapQ; | |
11 | |
12 float eta, q_r; | |
13 double *fk, *coef; | |
14 double *lhet; | |
15 struct __bmc_aux_t *aux; | |
16 } bam_maqcns_t; | |
17 | |
18 typedef struct { | |
19 int q_indel; | |
20 float r_indel; | |
21 // hidden parameters, unchangeable from command line | |
22 int mm_penalty, indel_err, ambi_thres; | |
23 } bam_maqindel_opt_t; | |
24 | |
25 typedef struct { | |
26 int indel1, indel2; | |
27 int cnt1, cnt2, cnt_anti; | |
28 int cnt_ref, cnt_ambi; | |
29 char *s[2]; | |
30 // | |
31 int gt, gl[2]; | |
32 int q_cns, q_ref; | |
33 } bam_maqindel_ret_t; | |
34 | |
35 #ifdef __cplusplus | |
36 extern "C" { | |
37 #endif | |
38 | |
39 bam_maqcns_t *bam_maqcns_init(); | |
40 void bam_maqcns_prepare(bam_maqcns_t *bm); | |
41 void bam_maqcns_destroy(bam_maqcns_t *bm); | |
42 glf1_t *bam_maqcns_glfgen(int n, const bam_pileup1_t *pl, uint8_t ref_base, bam_maqcns_t *bm); | |
43 uint32_t bam_maqcns_call(int n, const bam_pileup1_t *pl, bam_maqcns_t *bm); | |
44 // return: cns<<28 | cns2<<24 | mapQ<<16 | cnsQ<<8 | cnsQ2 | |
45 uint32_t glf2cns(const glf1_t *g, int q_r); | |
46 | |
47 bam_maqindel_opt_t *bam_maqindel_opt_init(); | |
48 bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, const bam_pileup1_t *pl, const char *ref, | |
49 int _n_types, int *_types); | |
50 void bam_maqindel_ret_destroy(bam_maqindel_ret_t*); | |
51 | |
52 #ifdef __cplusplus | |
53 } | |
54 #endif | |
55 | |
56 #endif |