Merge commit 'upstream/0.1.17'

[samtools.git] / bedidx.c

diff --git a/bedidx.c b/bedidx.c
index 92978318d4ccfbbabeeddd150458245f669062d8..34f0f2fb3ba0e40aaab31e4c8eca4140e4a5d458 100644 (file)
--- a/bedidx.c
+++ b/bedidx.c
@@ -4,6 +4,9 @@
 #include <stdio.h>
 #include <zlib.h>
 
+#include "ksort.h"
+KSORT_INIT_GENERIC(uint64_t)
+
 #include "kseq.h"
 KSTREAM_INIT(gzFile, gzread, 8192)
 
@@ -53,6 +56,7 @@ void bed_index(void *_h)
                if (kh_exist(h, k)) {
                        bed_reglist_t *p = &kh_val(h, k);
                        if (p->idx) free(p->idx);
+                       ks_introsort(uint64_t, p->n, p->a);
                        p->idx = bed_index_core(p->n, p->a, &p->m);
                }
        }
@@ -115,8 +119,10 @@ void *bed_read(const char *fn)
                        if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
                                beg = atoi(str->s); // begin
                                if (dret != '\n') {
-                                       if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0]))
+                                       if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
                                                end = atoi(str->s); // end
+                                               if (end < beg) end = -1;
+                                       }
                                }
                        }
                }