+#ifndef BAM2BCF_H
+#define BAM2BCF_H
+
+#include <stdint.h>
+#include "bcftools/bcf.h"
+
+struct __bcf_callaux_t;
+typedef struct __bcf_callaux_t bcf_callaux_t;
+
+typedef struct {
+ int depth, qsum[4];
+ int anno[16];
+ float p[25];
+} 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;
+ uint8_t *PL;
+} bcf_call_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+ 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);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif