* vcfutils.pl: fixed a typo in help message

[samtools.git] / bam_maqcns.c

diff --git a/bam_maqcns.c b/bam_maqcns.c
index 9caa5d7b4dfac43d166d163339547a82def69ca3..5715f9aafca24abad9e0cc17e2ef1f567e9f3fc8 100644 (file)
--- a/bam_maqcns.c
+++ b/bam_maqcns.c
@@ -110,7 +110,7 @@ bam_maqcns_t *bam_maqcns_init()
        bm = (bam_maqcns_t*)calloc(1, sizeof(bam_maqcns_t));
        bm->aux = (bmc_aux_t*)calloc(1, sizeof(bmc_aux_t));
        bm->het_rate = 0.001;
-       bm->theta = 0.85;
+       bm->theta = 0.83f;
        bm->n_hap = 2;
        bm->eta = 0.03;
        bm->cap_mapQ = 60;
@@ -461,7 +461,7 @@ bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, c
                for (i = 0; i < n_types; ++i) {
                        ka_param_t ap = ka_param_blast;
                        ap.band_width = 2 * types[n_types - 1] + 2;
-                       ap.gap_end = 0;
+                       ap.gap_end_ext = 0;
                        // write ref2
                        for (k = 0, j = left; j <= pos; ++j)
                                ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]];