From: Heng Li <lh3@live.co.uk>
Date: Tue, 5 May 2009 21:23:27 +0000 (+0000)
Subject:  * samtools-0.1.3-15 (r266)
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=5453d1b09f745d2e23e6394c2d329d19da7db061;p=samtools.git

 * samtools-0.1.3-15 (r266)
 * report an error if a non-* reference is present while @SQ is absent
---

diff --git a/bam_import.c b/bam_import.c
index fe9af91..77e3243 100644
--- a/bam_import.c
+++ b/bam_import.c
@@ -241,8 +241,12 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 	{ // flag, tid, pos, qual
 		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->flag = atoi(str->s);
 		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s);
-		if (c->tid < 0 && strcmp(str->s, "*"))
-			fprintf(stderr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s);
+		if (c->tid < 0 && strcmp(str->s, "*")) {
+			if (header->n_targets == 0) {
+				fprintf(stderr, "[sam_read1] missing header? Abort!\n");
+				exit(1);
+			} else fprintf(stderr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s);
+		}
 		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
 		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
 		if (ret < 0) return -2;
diff --git a/bamtk.c b/bamtk.c
index 316b128..31ef17c 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.3-14 (r262)"
+#define PACKAGE_VERSION "0.1.3-15 (r266)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);