X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.h;h=8ac6b79abfb60abaeefc29451923ec197c2f6c7a;hb=3a1bd4d97b4d58148b5a7fd845a3b6a023eecbed;hp=570990e4174caec6220c130e0c343dec1d6dd562;hpb=599bea10bc3487a0cbdf505e792a21a13fee2b11;p=samtools.git

diff --git a/bam2bcf.h b/bam2bcf.h
index 570990e..8ac6b79 100644
--- 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];
@@ -17,19 +24,24 @@ typedef struct __bcf_callaux_t {
 	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
@@ -40,9 +52,10 @@ 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);
+	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
 }