Imported Upstream version 0.5

[pysam.git] / samtools / bam_maqcns.h

diff --git a/samtools/bam_maqcns.h b/samtools/bam_maqcns.h
new file mode 100644 (file)
index 0000000..291ae53
--- /dev/null
+++ b/samtools/bam_maqcns.h
@@ -0,0 +1,61 @@
+#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