X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.h;h=b6514c05c2b5633a93104524bcd4fa8533c3ba80;hb=df7cadac556f302bdd0bc48c235c2b61b699dfe1;hp=92f104507952d5197a6bde2bd326ff16595cf558;hpb=98946f7c4842bc7c0429bb78982366ce46c70624;p=samtools.git

diff --git a/bam2bcf.h b/bam2bcf.h
index 92f1045..b6514c0 100644
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -16,8 +16,8 @@ typedef struct __bcf_callaux_t {
 } bcf_callaux_t;
 
 typedef struct {
-	int depth;
-	float indelreg, ins_len, del_len;
+	int depth, indelreg;
+	float ins_len, del_len;
 	int qsum[4];
 	int anno[16];
 	float p[25];
@@ -26,7 +26,9 @@ 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 indelreg;
+	float ins_len, del_len;
+	int depth, anno[16];
 	uint8_t *PL;
 } bcf_call_t;
 
@@ -38,6 +40,7 @@ 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_call_combine_gap(int n, const bcf_callret1_t *calls, 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);
 	int bcf_call_glfgen_gap(int pos, int _n, const bam_pileup1_t *pl, bcf_callaux_t *bca, bcf_callret1_t *r);