X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.h;h=26b022c08e89e3597bd6e400690d42bd7ecabe38;hb=95b7e2d5d54f2b10bef8dd937e43c342d2086b46;hp=570990e4174caec6220c130e0c343dec1d6dd562;hpb=599bea10bc3487a0cbdf505e792a21a13fee2b11;p=samtools.git

diff --git a/bam2bcf.h b/bam2bcf.h
index 570990e..26b022c 100644
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -17,10 +17,11 @@ typedef struct __bcf_callaux_t {
 	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];
 } bcf_callret1_t;
@@ -28,7 +29,7 @@ typedef struct {
 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;
 } bcf_call_t;
 
@@ -42,7 +43,8 @@ extern "C" {
 	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, 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);
+	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
 }