X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.h;h=655174f585f663b54c0e10327df45eddb8942616;hb=c0490a669e9f1f9257e4b02a263e92e842bf5357;hp=b96488b1ee29ed90b99bdad59f11e941a4c14cb7;hpb=67184476fcd4a7aba449556a2333586465fd6102;p=samtools.git

diff --git a/bam2bcf.h b/bam2bcf.h
index b96488b..655174f 100644
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -2,7 +2,7 @@
 #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;
@@ -10,11 +10,11 @@ typedef struct __bcf_callaux_t bcf_callaux_t;
 typedef struct {
 	int depth;
 	uint64_t sum_Q2;
-	float p[16], esum[4];
+	float p[25], esum[5];
 } 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;
 	uint8_t *PL;
@@ -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);