X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bedidx.c;h=ec75a1067f5905c69ead868ff42d2073189bb690;hp=92978318d4ccfbbabeeddd150458245f669062d8;hb=HEAD;hpb=0242bdf14e88f1058887598cbf898c0d0af01a82

diff --git a/bedidx.c b/bedidx.c
index 9297831..ec75a10 100644
--- a/bedidx.c
+++ b/bedidx.c
@@ -4,6 +4,13 @@
 #include <stdio.h>
 #include <zlib.h>
 
+#ifdef _WIN32
+#define drand48() ((double)rand() / RAND_MAX)
+#endif
+
+#include "ksort.h"
+KSORT_INIT_GENERIC(uint64_t)
+
 #include "kseq.h"
 KSTREAM_INIT(gzFile, gzread, 8192)
 
@@ -53,6 +60,7 @@ 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 +123,10 @@ 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;
+					}
 				}
 			}
 		}