* samtools-0.1.8-11 (r672)

[samtools.git] / bam2bcf.h

diff --git a/bam2bcf.h b/bam2bcf.h
index 3d9a8043a0b65bea590643b3ac34d9c07b214b89..73624c0a6bdc789d892aa4dc9d89ac07f7adcc38 100644 (file)
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -2,21 +2,23 @@
 #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;
+       int depth, d[4];
+       int dsum[2], d2sum[2];
        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 n, n_alleles, shift, ori_ref;
-       int depth, rmsQ;
+       int a[5]; // alleles: ref, alt, alt2, alt3
+       int n, n_alleles, shift, ori_ref, unseen;
+       int d[4], depth, rmsQ;
+       double davg[2], dstd[2];
        uint8_t *PL;
 } bcf_call_t;
 
@@ -24,7 +26,7 @@ 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);