X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.h;h=8ac6b79abfb60abaeefc29451923ec197c2f6c7a;hb=0ccd9d36ebf35ce620a8248ecf4336c84065e6c0;hp=4ea48095e3566ed1d55fa96bdcf873b4ba0da83f;hpb=ea1bf85308be7146d11a0153391d99fcfb3f83ad;p=samtools.git

diff --git a/bam2bcf.h b/bam2bcf.h
index 4ea4809..8ac6b79 100644
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -5,19 +5,22 @@
 #include "errmod.h"
 #include "bcftools/bcf.h"
 
-#define B2B_INDEL_NULL 0x7fff
-#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)
+#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];
-	int maxins, indelreg, last_mnp_pos;
+	int maxins, indelreg;
 	char *inscns;
 	uint16_t *bases;
 	errmod_t *e;
@@ -25,16 +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
-	int n, n_alleles, shift, ori_ref, unseen; // ori_ref can be B2B_REF_INDEL/B2B_REF_MNP
+    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
@@ -45,11 +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,
 						  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
 }