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view 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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#ifndef BAM_MAQCNS_H #define BAM_MAQCNS_H #include "glf.h" struct __bmc_aux_t; typedef struct { float het_rate, theta; int n_hap, cap_mapQ; float eta, q_r; double *fk, *coef; double *lhet; struct __bmc_aux_t *aux; } bam_maqcns_t; typedef struct { int q_indel; float r_indel; // hidden parameters, unchangeable from command line int mm_penalty, indel_err, ambi_thres; } bam_maqindel_opt_t; typedef struct { int indel1, indel2; int cnt1, cnt2, cnt_anti; int cnt_ref, cnt_ambi; char *s[2]; // int gt, gl[2]; int q_cns, q_ref; } bam_maqindel_ret_t; #ifdef __cplusplus extern "C" { #endif bam_maqcns_t *bam_maqcns_init(); void bam_maqcns_prepare(bam_maqcns_t *bm); void bam_maqcns_destroy(bam_maqcns_t *bm); glf1_t *bam_maqcns_glfgen(int n, const bam_pileup1_t *pl, uint8_t ref_base, bam_maqcns_t *bm); uint32_t bam_maqcns_call(int n, const bam_pileup1_t *pl, bam_maqcns_t *bm); // return: cns<<28 | cns2<<24 | mapQ<<16 | cnsQ<<8 | cnsQ2 uint32_t glf2cns(const glf1_t *g, int q_r); bam_maqindel_opt_t *bam_maqindel_opt_init(); bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, const bam_pileup1_t *pl, const char *ref, int _n_types, int *_types); void bam_maqindel_ret_destroy(bam_maqindel_ret_t*); #ifdef __cplusplus } #endif #endif