X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=blobdiff_plain;f=bam2bcf.h;h=92f104507952d5197a6bde2bd326ff16595cf558;hp=4de743a9287f7421e6f612a2426897d3dbe69212;hb=98946f7c4842bc7c0429bb78982366ce46c70624;hpb=48c105217263ffe19b676f6f6c918dc1c6f39c88

diff --git a/bam2bcf.h b/bam2bcf.h
index 4de743a..92f1045 100644
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -2,13 +2,23 @@
 #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 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, qsum[4];
+	int depth;
+	float indelreg, ins_len, del_len;
+	int qsum[4];
 	int anno[16];
 	float p[25];
 } bcf_callret1_t;
@@ -29,6 +39,7 @@ extern "C" {
 	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, 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
 }