X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_maqcns.h;fp=bam_maqcns.h;h=0000000000000000000000000000000000000000;hp=291ae533c3c38cd152b3c9c8fa8e820386a3718d;hb=b301e959d73eee0955c57004f344f17af00703f4;hpb=8a8212c76299ff302cdd41be704d8e0308bd2b1b

diff --git a/bam_maqcns.h b/bam_maqcns.h
deleted file mode 100644
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