* this revision is UNSTABLE

[samtools.git] / bam2bcf.h

diff --git a/bam2bcf.h b/bam2bcf.h
index 92f104507952d5197a6bde2bd326ff16595cf558..b6514c05c2b5633a93104524bcd4fa8533c3ba80 100644 (file)
--- 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);