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comparison pyPRADA_1.2/tools/samtools-0.1.16/bam2bcf.h @ 0:acc2ca1a3ba4

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author siyuan
date Thu, 20 Feb 2014 00:44:58 -0500
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-1:000000000000 0:acc2ca1a3ba4
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