# Uploaded samtools version 0.1.14-1.

[samtools.git] / bam_sort.c

diff --git a/bam_sort.c b/bam_sort.c
index 01f7016dd9a35ef27cf4cc232d7529b25d67880b..7aeccff3e1e8e61507c4983ce535de884d6bbcae 100644 (file)
--- 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);