Revert to r790. The recent changes are not good...

[samtools.git] / bam2bcf.h

diff --git a/bam2bcf.h b/bam2bcf.h
index b6514c05c2b5633a93104524bcd4fa8533c3ba80..4de743a9287f7421e6f612a2426897d3dbe69212 100644 (file)
--- 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
 }