# Install bcftools, its manpage, bcf-fix.pl, vcfutils.pl, and new examples.

[samtools.git] / bam_aux.c

diff --git a/bam_aux.c b/bam_aux.c
index d0d733fc467bfa9af7d2f032b83ffb47840ef18a..fbcd9822b233dab64f6c861fb332846acb951ce7 100644 (file)
--- a/bam_aux.c
+++ b/bam_aux.c
@@ -115,7 +115,7 @@ int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *be
        *ref_id = kh_value(h, iter);
        if (i == k) { /* dump the whole sequence */
                *begin = 0; *end = 1<<29; free(s);
-               return -1;
+               return 0;
        }
        for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
        *begin = atoi(p);
@@ -180,70 +180,3 @@ char *bam_aux2Z(const uint8_t *s)
        if (type == 'Z' || type == 'H') return (char*)s;
        else return 0;
 }
-
-/******************
- * rg2lib related *
- ******************/
-
-int bam_strmap_put(void *rg2lib, const char *rg, const char *lib)
-{
-       int ret;
-       khint_t k;
-       khash_t(r2l) *h = (khash_t(r2l)*)rg2lib;
-       char *key;
-       if (h == 0) return 1;
-       key = strdup(rg);
-       k = kh_put(r2l, h, key, &ret);
-       if (ret) kh_val(h, k) = strdup(lib);
-       else {
-               fprintf(stderr, "[bam_rg2lib_put] duplicated @RG ID: %s\n", rg);
-               free(key);
-       }
-       return 0;
-}
-
-const char *bam_strmap_get(const void *rg2lib, const char *rg)
-{
-       const khash_t(r2l) *h = (const khash_t(r2l)*)rg2lib;
-       khint_t k;
-       if (h == 0) return 0;
-       k = kh_get(r2l, h, rg);
-       if (k != kh_end(h)) return (const char*)kh_val(h, k);
-       else return 0;
-}
-
-void *bam_strmap_dup(const void *rg2lib)
-{
-       const khash_t(r2l) *h = (const khash_t(r2l)*)rg2lib;
-       khash_t(r2l) *g;
-       khint_t k, l;
-       int ret;
-       if (h == 0) return 0;
-       g = kh_init(r2l);
-       for (k = kh_begin(h); k < kh_end(h); ++k) {
-               if (kh_exist(h, k)) {
-                       char *key = strdup(kh_key(h, k));
-                       l = kh_put(r2l, g, key, &ret);
-                       kh_val(g, l) = strdup(kh_val(h, k));
-               }
-       }
-       return g;
-}
-
-void *bam_strmap_init()
-{
-       return (void*)kh_init(r2l);
-}
-
-void bam_strmap_destroy(void *rg2lib)
-{
-       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));
-               }
-       }
-       kh_destroy(r2l, h);
-}