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[samtools.git] / bam2bcf.h

diff --git a/bam2bcf.h b/bam2bcf.h
index f96a7e33719b08d003513d03e857df38ddb4dbf5..8ac6b79abfb60abaeefc29451923ec197c2f6c7a 100644 (file)
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -2,22 +2,46 @@
 #define BAM2BCF_H
 
 #include <stdint.h>
+#include "errmod.h"
 #include "bcftools/bcf.h"
 
-struct __bcf_callaux_t;
-typedef struct __bcf_callaux_t bcf_callaux_t;
+#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; // 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];
+       int maxins, indelreg;
+       char *inscns;
+       uint16_t *bases;
+       errmod_t *e;
+       void *rghash;
+} bcf_callaux_t;
 
 typedef struct {
-       int 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 anno[16], depth;
+       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
@@ -26,9 +50,12 @@ 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 /*4-bit*/, bcf_callaux_t *bca, bcf_callret1_t *r);
+       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 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);
 
 #ifdef __cplusplus
 }