Mercurial > repos > siyuan > prada
comparison pyPRADA_1.2/tools/samtools-0.1.16/bam2bcf.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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-1:000000000000 | 0:acc2ca1a3ba4 |
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1 #ifndef BAM2BCF_H | |
2 #define BAM2BCF_H | |
3 | |
4 #include <stdint.h> | |
5 #include "errmod.h" | |
6 #include "bcftools/bcf.h" | |
7 | |
8 #define B2B_INDEL_NULL 10000 | |
9 | |
10 typedef struct __bcf_callaux_t { | |
11 int capQ, min_baseQ; | |
12 int openQ, extQ, tandemQ; // for indels | |
13 int min_support; // for collecting indel candidates | |
14 double min_frac; // for collecting indel candidates | |
15 // for internal uses | |
16 int max_bases; | |
17 int indel_types[4]; | |
18 int maxins, indelreg; | |
19 char *inscns; | |
20 uint16_t *bases; | |
21 errmod_t *e; | |
22 void *rghash; | |
23 } bcf_callaux_t; | |
24 | |
25 typedef struct { | |
26 int depth, ori_depth, qsum[4]; | |
27 int anno[16]; | |
28 float p[25]; | |
29 } bcf_callret1_t; | |
30 | |
31 typedef struct { | |
32 int a[5]; // alleles: ref, alt, alt2, alt3 | |
33 int n, n_alleles, shift, ori_ref, unseen; | |
34 int anno[16], depth, ori_depth; | |
35 uint8_t *PL; | |
36 } bcf_call_t; | |
37 | |
38 #ifdef __cplusplus | |
39 extern "C" { | |
40 #endif | |
41 | |
42 bcf_callaux_t *bcf_call_init(double theta, int min_baseQ); | |
43 void bcf_call_destroy(bcf_callaux_t *bca); | |
44 int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r); | |
45 int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call); | |
46 int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP, | |
47 const bcf_callaux_t *bca, const char *ref); | |
48 int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref, | |
49 const void *rghash); | |
50 | |
51 #ifdef __cplusplus | |
52 } | |
53 #endif | |
54 | |
55 #endif |