X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam2bcf.h;h=4af080c4753b2070192bec5e04e16174ca5bb5f8;hp=0dddb924dcf62fee4f1352a9a20eecb7001da450;hb=HEAD;hpb=62781a2daa24d74a3c590e2669fad1fa7cabf933

diff --git a/bam2bcf.h b/bam2bcf.h
index 0dddb92..4af080c 100644
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -2,22 +2,39 @@
 #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 indels
+	int min_support; // for collecting indel candidates
+	double min_frac; // for collecting indel candidates
+	// for internal uses
+	int max_bases;
+	int indel_types[4];
+	int maxins, indelreg;
+	char *inscns;
+	uint16_t *bases;
+	errmod_t *e;
+	void *rghash;
+} bcf_callaux_t;
 
 typedef struct {
-	int depth, qsum[4];
+	int depth, ori_depth, qsum[4];
 	int anno[16];
 	float p[25];
+    int mvd[3]; // mean variant distance, number of variant reads, average read length
 } bcf_callret1_t;
 
 typedef struct {
 	int a[5]; // alleles: ref, alt, alt2, alt3
 	int n, n_alleles, shift, ori_ref, unseen;
-	int anno[16], depth;
+	int anno[16], depth, ori_depth;
 	uint8_t *PL;
+    float vdb; // variant distance bias
 } bcf_call_t;
 
 #ifdef __cplusplus
@@ -26,9 +43,12 @@ 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);
+	int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP,
+					 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
 }