X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.h;h=0dddb924dcf62fee4f1352a9a20eecb7001da450;hb=3f13738c659d0b49fe7ac99145cdc9fa2f507af4;hp=b96488b1ee29ed90b99bdad59f11e941a4c14cb7;hpb=67184476fcd4a7aba449556a2333586465fd6102;p=samtools.git

diff --git a/bam2bcf.h b/bam2bcf.h
index b96488b..0dddb92 100644
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -2,21 +2,21 @@
 #define BAM2BCF_H
 
 #include <stdint.h>
-#include "bcf.h"
+#include "bcftools/bcf.h"
 
 struct __bcf_callaux_t;
 typedef struct __bcf_callaux_t bcf_callaux_t;
 
 typedef struct {
-	int depth;
-	uint64_t sum_Q2;
-	float p[16], esum[4];
+	int depth, qsum[4];
+	int anno[16];
+	float p[25];
 } bcf_callret1_t;
 
 typedef struct {
-	int a[4]; // alleles: ref, alt, alt2, alt3
+	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;
 
@@ -24,7 +24,7 @@ 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_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call);