Added notes on how the package is tested.

[samtools.git] / bam_color.c

diff --git a/bam_color.c b/bam_color.c
index 75aedd603a1798e85a40c982dd9392ee2a3e5b3f..ce637f708db56de777e86f2f0ad50478fb1a6657 100644 (file)
--- a/bam_color.c
+++ b/bam_color.c
@@ -100,8 +100,8 @@ char bam_aux_getCEi(bam1_t *b, int i)
                cs_i = strlen(cs) - 1 - i;
                // get current color
                cur_color = cs[cs_i];
-               // get previous base
-               prev_b = (0 == cs_i) ? cs[0] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i+1)];
+               // get previous base.  Note: must rc adaptor
+               prev_b = (cs_i == 1) ? "TGCAN"[(int)bam_aux_nt2int(cs[0])] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i+1)];
                // get current base
                cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)]; 
        }