X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.h;h=b2b1825cd59a17a1973b040f722f1efb13ef24f0;hb=28391e5898804ce6b805016d8c676fdf61442eb3;hp=3d9a8043a0b65bea590643b3ac34d9c07b214b89;hpb=7eaf231bcd3c44fad56f8d7200e44a37ae453c88;p=samtools.git

diff --git a/bam2bcf.h b/bam2bcf.h
index 3d9a804..b2b1825 100644
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -2,33 +2,63 @@
 #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
+
+#define B2B_FMT_DP 0x1
+#define B2B_FMT_SP 0x2
+#define B2B_FMT_DV 0x4
+
+typedef struct __bcf_callaux_t {
+	int capQ, min_baseQ;
+	int openQ, extQ, tandemQ; // for indels
+	int min_support, max_support; // for collecting indel candidates
+	double min_frac, max_frac; // for collecting indel candidates
+    int per_sample_flt; // indel filtering strategy
+    int *ref_pos, *alt_pos, npos; // for ReadPosBias
+	// for internal uses
+	int max_bases;
+	int indel_types[4];
+	int maxins, indelreg;
+    int read_len;
+	char *inscns;
+	uint16_t *bases;
+	errmod_t *e;
+	void *rghash;
+} bcf_callaux_t;
 
 typedef struct {
-	int depth;
-	uint64_t sum_Q2;
-	float p[16], esum[4];
+	int depth, n_supp, ori_depth, qsum[4];
+	unsigned int anno[16];
+	float p[25];
 } bcf_callret1_t;
 
 typedef struct {
-	int a[4]; // alleles: ref, alt, alt2, alt3
-	int n, n_alleles, shift, ori_ref;
-	int depth, rmsQ;
+	int a[5]; // alleles: ref, alt, alt2, alt3
+    float qsum[4];
+	int n, n_alleles, shift, ori_ref, unseen;
+	int n_supp; // number of supporting non-reference reads
+	unsigned int anno[16], depth, ori_depth;
 	uint8_t *PL;
+    float vdb; // variant distance bias
+    float read_pos_bias;
+    struct { float avg, var; int dp; } read_pos;
 } bcf_call_t;
 
 #ifdef __cplusplus
 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_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_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, bcf_callaux_t *bca, 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 fmt_flag,
+					 const bcf_callaux_t *bca, const char *ref);
+	int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
+						  const void *rghash);
 
 #ifdef __cplusplus
 }