X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_sort.c;h=7aeccff3e1e8e61507c4983ce535de884d6bbcae;hp=01f7016dd9a35ef27cf4cc232d7529b25d67880b;hb=ced7709f121a00d5049d99ee8576037994aab1d1;hpb=78c7059ff49802b06e7318fb6ad9a0908e80903b

diff --git a/bam_sort.c b/bam_sort.c
index 01f7016..7aeccff 100644
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -222,8 +222,11 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
 	ks_heapmake(heap, n, heap);
 	while (heap->pos != HEAP_EMPTY) {
 		bam1_t *b = heap->b;
-		if ((flag & MERGE_RG) && bam_aux_get(b, "RG") == 0)
+		if (flag & MERGE_RG) {
+			uint8_t *rg = bam_aux_get(b, "RG");
+			if (rg) bam_aux_del(b, rg);
 			bam_aux_append(b, "RG", 'Z', RG_len[heap->i] + 1, (uint8_t*)RG[heap->i]);
+		}
 		bam_write1_core(fpout, &b->core, b->data_len, b->data);
 		if ((j = bam_iter_read(fp[heap->i], iter[heap->i], b)) >= 0) {
 			heap->pos = ((uint64_t)b->core.tid<<32) | (uint32_t)b->core.pos<<1 | bam1_strand(b);
@@ -295,14 +298,19 @@ KSORT_INIT(sort, bam1_p, bam1_lt)
 
 static void sort_blocks(int n, int k, bam1_p *buf, const char *prefix, const bam_header_t *h, int is_stdout)
 {
-	char *name;
+	char *name, mode[3];
 	int i;
 	bamFile fp;
 	ks_mergesort(sort, k, buf, 0);
 	name = (char*)calloc(strlen(prefix) + 20, 1);
-	if (n >= 0) sprintf(name, "%s.%.4d.bam", prefix, n);
-	else sprintf(name, "%s.bam", prefix);
-	fp = is_stdout? bam_dopen(fileno(stdout), "w") : bam_open(name, "w");
+	if (n >= 0) {
+		sprintf(name, "%s.%.4d.bam", prefix, n);
+		strcpy(mode, "w1");
+	} else {
+		sprintf(name, "%s.bam", prefix);
+		strcpy(mode, "w");
+	}
+	fp = is_stdout? bam_dopen(fileno(stdout), mode) : bam_open(name, mode);
 	if (fp == 0) {
 		fprintf(stderr, "[sort_blocks] fail to create file %s.\n", name);
 		free(name);