- int cs_i;
- uint8_t *c = bam_aux_get(b, "CS");
- char *cs = NULL;
- char prev_b, cur_b;
- char cur_color, cor_color;
-
- // return the base if the tag was not found
- if(0 == c) return 0;
-
- cs = bam_aux2Z(c);
-
- // adjust for strandedness and leading adaptor
- if(bam1_strand(b)) { //reverse strand
- 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 current base
- cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)];
- }
- else {
- cs_i=i+1;
- // get current color
- cur_color = cs[cs_i];
- // get previous base
- prev_b = (0 == i) ? 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)];
- }
-
- // corrected color
- cor_color = bam_aux_ntnt2cs(prev_b, cur_b);
-
- if(cur_color == cor_color) {
- return '-';
- }
- else {
- return cur_color;
+ khash_t(r2l) *h = (khash_t(r2l)*)rg2lib;
+ khint_t k;
+ if (h == 0) return;
+ for (k = kh_begin(h); k < kh_end(h); ++k) {
+ if (kh_exist(h, k)) {
+ free((char*)kh_key(h, k)); free(kh_val(h, k));
+ }