X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.h;h=4de743a9287f7421e6f612a2426897d3dbe69212;hb=896d270d34b71e0422ddca4a0d62136cb2e537be;hp=ddc6b6146fb4e9daab037bd61197b2a1ab21de2d;hpb=6dc53c5ab2964e68e8936850d2339d047d2433ef;p=samtools.git

diff --git a/bam2bcf.h b/bam2bcf.h
index ddc6b61..4de743a 100644
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -8,15 +8,15 @@ struct __bcf_callaux_t;
 typedef struct __bcf_callaux_t bcf_callaux_t;
 
 typedef struct {
-	int depth, d[4], ed[4], qsum[4];
-	uint64_t sum_Q2;
+	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 d[4], ed[4], depth, rmsQ;
+	int anno[16], depth;
 	uint8_t *PL;
 } bcf_call_t;
 
@@ -28,7 +28,7 @@ extern "C" {
 	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);
+	int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP);
 
 #ifdef __cplusplus
 }