X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.h;h=4de743a9287f7421e6f612a2426897d3dbe69212;hb=2d2be1edb0548e95b771bc9c79cff48eb5d2e1f5;hp=b6514c05c2b5633a93104524bcd4fa8533c3ba80;hpb=df7cadac556f302bdd0bc48c235c2b61b699dfe1;p=samtools.git

diff --git a/bam2bcf.h b/bam2bcf.h
index b6514c0..4de743a 100644
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -2,23 +2,13 @@
 #define BAM2BCF_H
 
 #include <stdint.h>
-#include "errmod.h"
 #include "bcftools/bcf.h"
 
-#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;
+struct __bcf_callaux_t;
+typedef struct __bcf_callaux_t bcf_callaux_t;
 
 typedef struct {
-	int depth, indelreg;
-	float ins_len, del_len;
-	int qsum[4];
+	int depth, qsum[4];
 	int anno[16];
 	float p[25];
 } bcf_callret1_t;
@@ -26,9 +16,7 @@ typedef struct {
 typedef struct {
 	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];
+	int anno[16], depth;
 	uint8_t *PL;
 } bcf_call_t;
 
@@ -40,9 +28,7 @@ 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_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
 }