Mercurial > repos > siyuan > prada
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pyPRADA_1.2/tools/samtools-0.1.16/bam2bcf.h Thu Feb 20 00:44:58 2014 -0500 @@ -0,0 +1,55 @@ +#ifndef BAM2BCF_H +#define BAM2BCF_H + +#include <stdint.h> +#include "errmod.h" +#include "bcftools/bcf.h" + +#define B2B_INDEL_NULL 10000 + +typedef struct __bcf_callaux_t { + int capQ, min_baseQ; + int openQ, extQ, tandemQ; // for indels + int min_support; // for collecting indel candidates + double min_frac; // for collecting indel candidates + // for internal uses + int max_bases; + int indel_types[4]; + int maxins, indelreg; + char *inscns; + uint16_t *bases; + errmod_t *e; + void *rghash; +} bcf_callaux_t; + +typedef struct { + int depth, ori_depth, qsum[4]; + int anno[16]; + float p[25]; +} bcf_callret1_t; + +typedef struct { + int a[5]; // alleles: ref, alt, alt2, alt3 + int n, n_alleles, shift, ori_ref, unseen; + int anno[16], depth, ori_depth; + uint8_t *PL; +} bcf_call_t; + +#ifdef __cplusplus +extern "C" { +#endif + + bcf_callaux_t *bcf_call_init(double theta, int min_baseQ); + void bcf_call_destroy(bcf_callaux_t *bca); + int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r); + int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call); + int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP, + const bcf_callaux_t *bca, const char *ref); + int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref, + const void *rghash); + +#ifdef __cplusplus +} +#endif + +#endif