* samtools-0.1.9-2 (r797)

[samtools.git] / bam2bcf.h

diff --git a/bam2bcf.h b/bam2bcf.h
index e39ab7bfe90a6a6ec2a51f27e1325c32a1e4f2b5..570990e4174caec6220c130e0c343dec1d6dd562 100644 (file)
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -13,6 +13,8 @@ typedef struct __bcf_callaux_t {
        // for internal uses
        int max_bases;
        int indel_types[4];
+       int maxins, indelreg;
+       char *inscns;
        uint16_t *bases;
        errmod_t *e;
 } bcf_callaux_t;
@@ -38,7 +40,8 @@ extern "C" {
        void bcf_call_destroy(bcf_callaux_t *bca);
        int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, 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, bcf_callret1_t *bcr, int is_SP);
+       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);
 
 #ifdef __cplusplus