Release samtools-0.1.16 (r963:234)

[samtools.git] / bam_maqcns.h

diff --git a/bam_maqcns.h b/bam_maqcns.h
index 5d410ef9fda607ba3f02a925522c4aa59864cf25..291ae533c3c38cd152b3c9c8fa8e820386a3718d 100644 (file)
--- a/bam_maqcns.h
+++ b/bam_maqcns.h
@@ -3,11 +3,15 @@
 
 #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;
+       int n_hap, cap_mapQ, errmod, min_baseQ;
 
        float eta, q_r;
        double *fk, *coef;
@@ -16,13 +20,21 @@ typedef struct {
 } 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_ambi, cnt_anti;
-       char *s1, *s2;
+       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
@@ -38,7 +50,8 @@ extern "C" {
        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);
+       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