prepare for the indel caller. It is not ready yet.

[samtools.git] / bam2bcf.c

diff --git a/bam2bcf.c b/bam2bcf.c
index 509761d3395df7d01e56f7a368f2f2daa29be4b3..fa9d7a47b762235ff6ea0a212c01b0c406bee301 100644 (file)
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -14,18 +14,13 @@ extern      void ks_introsort_uint32_t(size_t n, uint32_t a[]);
 
 #define CAP_DIST 25
 
-struct __bcf_callaux_t {
-       int max_bases, capQ, min_baseQ;
-       uint16_t *bases;
-       errmod_t *e;
-};
-
 bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
 {
        bcf_callaux_t *bca;
        if (theta <= 0.) theta = CALL_DEFTHETA;
        bca = calloc(1, sizeof(bcf_callaux_t));
        bca->capQ = 60;
+       bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 70;
        bca->min_baseQ = min_baseQ;
        bca->e = errmod_init(1. - theta);
        return bca;