Allow tabs in the CO header field

[samtools.git] / bam_maqcns.h

diff --git a/bam_maqcns.h b/bam_maqcns.h
index 5d410ef9fda607ba3f02a925522c4aa59864cf25..fa5489d13caad7c5c20489091302bfb5b2a5799d 100644 (file)
--- a/bam_maqcns.h
+++ b/bam_maqcns.h
@@ -7,7 +7,7 @@ struct __bmc_aux_t;
 
 typedef struct {
        float het_rate, theta;
-       int n_hap;
+       int n_hap, cap_mapQ, is_soap;
 
        float eta, q_r;
        double *fk, *coef;
@@ -16,13 +16,20 @@ typedef struct {
 } 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_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 +45,8 @@ 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