* Merge from branches/dev/

[samtools.git] / bam_import.c

diff --git a/bam_import.c b/bam_import.c
index 6b3b4bc69352a92d0c9e74379fe8ddd2e4564c43..4b7bb2122e0e046bf65874bdda27e03828479b06 100644 (file)
--- a/bam_import.c
+++ b/bam_import.c
@@ -245,9 +245,9 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
                        type = str->s[3];
                        s = alloc_data(b, doff + 3) + doff;
                        s[0] = key[0]; s[1] = key[1]; s += 2; doff += 2;
-                       if (type == 'A' || type == 'a') {
+                       if (type == 'A' || type == 'a' || type == 'c' || type == 'C') { // c and C for backward compatibility
                                s = alloc_data(b, doff + 2) + doff;
-                               *s++ = type; *s = str->s[5];
+                               *s++ = 'A'; *s = str->s[5];
                                doff += 2;
                        } else if (type == 'I' || type == 'i') {
                                long long x;
@@ -341,7 +341,7 @@ static void taf2baf_core(const char *fntaf, const char *fnbaf, bam_header_t *hea
        int ret;
 
        b = (bam1_t*)calloc(1, sizeof(bam1_t));
-       fpbaf = bam_open(fnbaf, "w");
+       fpbaf = (strcmp(fnbaf, "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(fnbaf, "w");
        fp = sam_open(fntaf);
        ret = sam_read1(fp, header, b);
        bam_header_write(fpbaf, header);