indel calling is apparently working, but more information needs to be collected

[samtools.git] / bam2bcf.h

diff --git a/bam2bcf.h b/bam2bcf.h
index 89f4fa130886e388c18f5989b2c2b5bd33138526..e39ab7bfe90a6a6ec2a51f27e1325c32a1e4f2b5 100644 (file)
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -2,21 +2,31 @@
 #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 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;
-       uint64_t sum_Q2;
-       float p[25], esum[5];
+       int depth, qsum[4];
+       int anno[16];
+       float p[25];
 } bcf_callret1_t;
 
 typedef struct {
        int a[5]; // alleles: ref, alt, alt2, alt3
        int n, n_alleles, shift, ori_ref, unseen;
-       int depth, rmsQ;
+       int anno[16], depth;
        uint8_t *PL;
 } bcf_call_t;
 
@@ -24,11 +34,12 @@ 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_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);
+       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
 }