X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.h;h=94207d092e151f48b64d2380e1e71c1493f2e155;hb=0bb4884ffb1f4c9485efee763dd63b575f2c1381;hp=73624c0a6bdc789d892aa4dc9d89ac07f7adcc38;hpb=cbe42056eafe54cb371f61f6360bef670b51a3da;p=samtools.git

diff --git a/bam2bcf.h b/bam2bcf.h
index 73624c0..94207d0 100644
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -2,23 +2,31 @@
 #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
+
+typedef struct __bcf_callaux_t {
+	int capQ, min_baseQ;
+	int openQ, extQ, tandemQ;
+	// for internal uses
+	int max_bases;
+	int indel_types[4];
+	uint16_t *bases;
+	errmod_t *e;
+} bcf_callaux_t;
 
 typedef struct {
-	int depth, d[4];
-	int dsum[2], d2sum[2];
-	uint64_t sum_Q2;
-	float p[25], esum[5];
+	int depth, qsum[4];
+	int anno[16];
+	float p[25];
 } bcf_callret1_t;
 
 typedef struct {
 	int a[5]; // alleles: ref, alt, alt2, alt3
 	int n, n_alleles, shift, ori_ref, unseen;
-	int d[4], depth, rmsQ;
-	double davg[2], dstd[2];
+	int anno[16], depth;
 	uint8_t *PL;
 } bcf_call_t;
 
@@ -30,7 +38,8 @@ extern "C" {
 	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_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);
+	int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP);
+	int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref);
 
 #ifdef __cplusplus
 }