added the ace2sam converter

[samtools.git] / bam2bcf.h

diff --git a/bam2bcf.h b/bam2bcf.h
index 0de76f99afa54461fe3a74416098182d2471bdfa..4af080c4753b2070192bec5e04e16174ca5bb5f8 100644 (file)
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -6,18 +6,16 @@
 #include "bcftools/bcf.h"
 
 #define B2B_INDEL_NULL 10000
-#define B2B_MAX_MNP    4 // cannot be larger than 4!!!
-#define B2B_MNP_WIN    10
-#define B2B_REF_INDEL  (-1)
-#define B2B_REF_MNP    (-2)
 
 typedef struct __bcf_callaux_t {
        int capQ, min_baseQ;
-       int openQ, extQ, tandemQ;
+       int openQ, extQ, tandemQ; // for indels
+       int min_support; // for collecting indel candidates
+       double min_frac; // for collecting indel candidates
        // for internal uses
        int max_bases;
        int indel_types[4];
-       int maxins, indelreg, last_mnp_pos;
+       int maxins, indelreg;
        char *inscns;
        uint16_t *bases;
        errmod_t *e;
@@ -28,13 +26,15 @@ typedef struct {
        int depth, ori_depth, qsum[4];
        int anno[16];
        float p[25];
+    int mvd[3]; // mean variant distance, number of variant reads, average read length
 } bcf_callret1_t;
 
 typedef struct {
        int a[5]; // alleles: ref, alt, alt2, alt3
-       int n, n_alleles, shift, ori_ref, unseen; // ori_ref can be B2B_REF_INDEL/B2B_REF_MNP
+       int n, n_alleles, shift, ori_ref, unseen;
        int anno[16], depth, ori_depth;
        uint8_t *PL;
+    float vdb; // variant distance bias
 } bcf_call_t;
 
 #ifdef __cplusplus
@@ -49,7 +49,6 @@ extern "C" {
                                         const bcf_callaux_t *bca, const char *ref);
        int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
                                                  const void *rghash);
-       int bcf_call_mnp_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref);
 
 #ifdef __cplusplus
 }