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[samtools.git] / bam2bcf.h

diff --git a/bam2bcf.h b/bam2bcf.h
index 26b022c08e89e3597bd6e400690d42bd7ecabe38..8ac6b79abfb60abaeefc29451923ec197c2f6c7a 100644 (file)
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -7,9 +7,16 @@
 
 #define B2B_INDEL_NULL 10000
 
+#define B2B_FMT_DP 0x1
+#define B2B_FMT_SP 0x2
+#define B2B_FMT_DV 0x4
+
 typedef struct __bcf_callaux_t {
        int capQ, min_baseQ;
-       int openQ, extQ, tandemQ;
+       int openQ, extQ, tandemQ; // for indels
+       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
        // for internal uses
        int max_bases;
        int indel_types[4];
@@ -21,16 +28,20 @@ typedef struct __bcf_callaux_t {
 } bcf_callaux_t;
 
 typedef struct {
-       int depth, ori_depth, qsum[4];
+       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 {
        int a[5]; // alleles: ref, alt, alt2, alt3
+    float qsum[4];
        int n, n_alleles, shift, ori_ref, unseen;
+       int n_supp; // number of supporting non-reference reads
        int anno[16], depth, ori_depth;
        uint8_t *PL;
+    float vdb; // variant distance bias
 } bcf_call_t;
 
 #ifdef __cplusplus
@@ -41,7 +52,7 @@ extern "C" {
        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_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP,
+       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,
                                                  const void *rghash);