Imported Upstream version 0.1.17

[samtools.git] / bam_maqcns.h

diff --git a/bam_maqcns.h b/bam_maqcns.h
deleted file mode 100644 (file)
index 291ae53..0000000
--- a/bam_maqcns.h
+++ /dev/null
@@ -1,61 +0,0 @@
-#ifndef BAM_MAQCNS_H
-#define BAM_MAQCNS_H
-
-#include "glf.h"
-
-#define BAM_ERRMOD_MAQ2 0
-#define BAM_ERRMOD_MAQ  1
-#define BAM_ERRMOD_SOAP 2
-
-struct __bmc_aux_t;
-
-typedef struct {
-       float het_rate, theta;
-       int n_hap, cap_mapQ, errmod, min_baseQ;
-
-       float eta, q_r;
-       double *fk, *coef;
-       double *lhet;
-       struct __bmc_aux_t *aux;
-} bam_maqcns_t;
-
-typedef struct {
-       int q_indel; // indel sequencing error, phred scaled
-       float r_indel; // indel prior
-       float r_snp; // snp prior
-       // 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