X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.h;h=e39ab7bfe90a6a6ec2a51f27e1325c32a1e4f2b5;hb=917ed8ca3a137ff2c2db887c0c72f3cce09f7df4;hp=4de743a9287f7421e6f612a2426897d3dbe69212;hpb=2d2be1edb0548e95b771bc9c79cff48eb5d2e1f5;p=samtools.git

diff --git a/bam2bcf.h b/bam2bcf.h
index 4de743a..e39ab7b 100644
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -2,10 +2,20 @@
 #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, qsum[4];
@@ -26,9 +36,10 @@ extern "C" {
 
 	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_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_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref);
 
 #ifdef __cplusplus
 }