New upstream release.

[samtools.git] / sample.c

diff --git a/sample.c b/sample.c
index 3efc559dfda52ff5b8a706feb4036a79a7d1c6f8..830b9d1cb9f1aad1230c82dd8d24ad958645c7ff 100644 (file)
--- a/sample.c
+++ b/sample.c
@@ -52,10 +52,15 @@ static void add_pair(bam_sample_t *sm, khash_t(sm) *sm2id, const char *key, cons
 int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt)
 {
        const char *p = txt, *q, *r;
-       kstring_t buf;
+       kstring_t buf, first_sm;
        int n = 0;
        khash_t(sm) *sm2id = (khash_t(sm)*)sm->sm2id;
+       if (txt == 0) {
+               add_pair(sm, sm2id, fn, fn);
+               return 0;
+       }
        memset(&buf, 0, sizeof(kstring_t));
+    memset(&first_sm, 0, sizeof(kstring_t));
        while ((q = strstr(p, "@RG")) != 0) {
                p = q + 3;
                r = q = 0;
@@ -69,12 +74,21 @@ int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt)
                        oq = *u; or = *v; *u = *v = '\0';
                        buf.l = 0; kputs(fn, &buf); kputc('/', &buf); kputs(q, &buf);
                        add_pair(sm, sm2id, buf.s, r);
+            if ( !first_sm.s )
+                kputs(r,&first_sm); 
                        *u = oq; *v = or;
                } else break;
                p = q > r? q : r;
                ++n;
        }
        if (n == 0) add_pair(sm, sm2id, fn, fn);
+    // If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but
+    //  use the tag instead.
+    else if ( n==1 && first_sm.s )
+        add_pair(sm,sm2id,fn,first_sm.s);
+    if ( first_sm.s )
+        free(first_sm.s);
+
 //     add_pair(sm, sm2id, fn, fn);
        free(buf.s);
        return 0;