* samtools-0.1.2-24

 * in merge, gives a warning rather than error if the target sequence length is different
 * allow empty header

bam.c

@@ -102,7 +102,6 @@ bam_header_t *bam_header_read(bamFile fp)
 	bam_read(fp, header->text, header->l_text);
 	bam_read(fp, &header->n_targets, 4);
 	if (bam_is_be) bam_swap_endian_4p(&header->n_targets);
-	assert(header->n_targets > 0);
 	// read reference sequence names and lengths
 	header->target_name = (char**)calloc(header->n_targets, sizeof(char*));
 	header->target_len = (uint32_t*)calloc(header->n_targets, 4);

bam_import.c

@@ -102,7 +102,7 @@ bam_header_t *sam_header_read2(const char *fn)
 	assert(fp);
 	ks = ks_init(fp);
 	str = (kstring_t*)calloc(1, sizeof(kstring_t));
-	while (ks_getuntil(ks, 0, str, &dret) >= 0) {
+	while (ks_getuntil(ks, 0, str, &dret) > 0) {
 		char *s = strdup(str->s);
 		int len, i;
 		i = kh_size(hash);

bam_sort.c

@@ -66,13 +66,17 @@ void bam_merge_core(int by_qname, const char *out, int n, char * const *fn)
 		else { // validate multiple baf
 			if (hout->n_targets != hin->n_targets) {
 				fprintf(stderr, "[bam_merge_core] file '%s' has different number of target sequences. Abort!\n", fn[i]);
-				abort();
+				exit(1);
 			}
 			for (j = 0; j < hout->n_targets; ++j) {
-				if (strcmp(hout->target_name[j], hin->target_name[j]) || hout->target_len[j] != hin->target_len[j]) {
-					fprintf(stderr, "[bam_merge_core] file '%s' has a different target sequence. Abort!\n", fn[i]);
-					abort();
+				if (strcmp(hout->target_name[j], hin->target_name[j])) {
+					fprintf(stderr, "[bam_merge_core] different target sequence name: '%s' != '%s' in file '%s'. Abort!\n",
+							hout->target_name[j], hin->target_name[j], fn[i]);
+					exit(1);
 				}
+				if (hout->target_len[j] != hin->target_len[j])
+					fprintf(stderr, "[bam_merge_core] different target sequence length: %d != %d in file '%s'. Continue.\n",
+							hout->target_len[j], hin->target_len[j], fn[i]);
 			}
 			bam_header_destroy(hin);
 		}

bamtk.c

@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.2-23"
+#define PACKAGE_VERSION "0.1.2-24"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

kseq.h

@@ -128,6 +128,10 @@ typedef struct __kstring_t {
 				break;													\
 			}															\
 		}																\
+		if (str->l == 0) {												\
+			str->m = 1;													\
+			str->s = (char*)calloc(1, 1);								\
+		}																\
 		str->s[str->l] = '\0';											\
 		return str->l;													\
 	}