backup commit

[samtools.git] / bam2bcf.h

diff --git a/bam2bcf.h b/bam2bcf.h
index 8ac6b79abfb60abaeefc29451923ec197c2f6c7a..46f91f9c7ad282ad033ce6391461b18f34d83496 100644 (file)
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -17,10 +17,12 @@ typedef struct __bcf_callaux_t {
        int min_support, max_support; // for collecting indel candidates
        double min_frac, max_frac; // for collecting indel candidates
     int per_sample_flt; // indel filtering strategy
+    int *ref_pos, *alt_pos, npos; // for ReadPosBias
        // for internal uses
        int max_bases;
        int indel_types[4];
        int maxins, indelreg;
+    int read_len;
        char *inscns;
        uint16_t *bases;
        errmod_t *e;
@@ -31,7 +33,6 @@ typedef struct {
        int depth, n_supp, 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 {
@@ -42,6 +43,7 @@ typedef struct {
        int anno[16], depth, ori_depth;
        uint8_t *PL;
     float vdb; // variant distance bias
+    float read_pos_bias;
 } bcf_call_t;
 
 #ifdef __cplusplus
@@ -51,7 +53,7 @@ extern "C" {
        bcf_callaux_t *bcf_call_init(double theta, int min_baseQ);
        void bcf_call_destroy(bcf_callaux_t *bca);
        int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r);
-       int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call);
+       int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int ref_base /*4-bit*/, bcf_call_t *call);
        int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int fmt_flag,
                                         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,