X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bedidx.c;h=ec75a1067f5905c69ead868ff42d2073189bb690;hb=70c740facc966321754c6bfcc6d61ea056480638;hp=9b76af74ac71302521a8c01b0a100d8d8e1e904d;hpb=674ffee7adcfc928f5039777180206fdebc5539b;p=samtools.git

diff --git a/bedidx.c b/bedidx.c
index 9b76af7..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)
 
@@ -26,7 +33,7 @@ int *bed_index_core(int n, uint64_t *a, int *n_idx)
 	m = *n_idx = 0; idx = 0;
 	for (i = 0; i < n; ++i) {
 		int beg, end;
-		beg = a[i]>>32; end = (uint32_t)a[i];
+		beg = a[i]>>32 >> LIDX_SHIFT; end = ((uint32_t)a[i]) >> LIDX_SHIFT;
 		if (m < end + 1) {
 			int oldm = m;
 			m = end + 1;
@@ -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);
 		}
 	}
@@ -96,8 +104,9 @@ void *bed_read(const char *fn)
 	int dret;
 	kstring_t *str;
 	// read the list
-	str = calloc(1, sizeof(kstring_t));
 	fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+	if (fp == 0) return 0;
+	str = calloc(1, sizeof(kstring_t));
 	ks = ks_init(fp);
 	while (ks_getuntil(ks, 0, str, &dret) >= 0) { // read the chr name
 		int beg = -1, end = -1;
@@ -114,8 +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;
+					}
 				}
 			}
 		}