X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.h;h=b6514c05c2b5633a93104524bcd4fa8533c3ba80;hb=df7cadac556f302bdd0bc48c235c2b61b699dfe1;hp=3d9a8043a0b65bea590643b3ac34d9c07b214b89;hpb=7eaf231bcd3c44fad56f8d7200e44a37ae453c88;p=samtools.git

diff --git a/bam2bcf.h b/bam2bcf.h
index 3d9a804..b6514c0 100644
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -2,21 +2,33 @@
 #define BAM2BCF_H
 
 #include <stdint.h>
-#include "bcf.h"
+#include "errmod.h"
+#include "bcftools/bcf.h"
 
-struct __bcf_callaux_t;
-typedef struct __bcf_callaux_t bcf_callaux_t;
+#define BAM2BCF_INDELREG_THRES 13
+
+typedef struct __bcf_callaux_t {
+	int max_bases, capQ, min_baseQ;
+	int openQ, extQ, tandemQ;
+	// for internal uses
+	uint16_t *bases;
+	errmod_t *e;
+} bcf_callaux_t;
 
 typedef struct {
-	int depth;
-	uint64_t sum_Q2;
-	float p[16], esum[4];
+	int depth, indelreg;
+	float ins_len, del_len;
+	int qsum[4];
+	int anno[16];
+	float p[25];
 } bcf_callret1_t;
 
 typedef struct {
-	int a[4]; // alleles: ref, alt, alt2, alt3
-	int n, n_alleles, shift, ori_ref;
-	int depth, rmsQ;
+	int a[5]; // alleles: ref, alt, alt2, alt3
+	int n, n_alleles, shift, ori_ref, unseen;
+	int indelreg;
+	float ins_len, del_len;
+	int depth, anno[16];
 	uint8_t *PL;
 } bcf_call_t;
 
@@ -24,11 +36,13 @@ typedef struct {
 extern "C" {
 #endif
 
-	bcf_callaux_t *bcf_call_init(double theta);
+	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_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_call_combine_gap(int n, const bcf_callret1_t *calls, 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_call_glfgen_gap(int pos, int _n, const bam_pileup1_t *pl, bcf_callaux_t *bca, bcf_callret1_t *r);
 
 #ifdef __cplusplus
 }