X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sample.c;h=830b9d1cb9f1aad1230c82dd8d24ad958645c7ff;hb=9f118264ea012adc21a46d7c03eaad4f9ce7d4d4;hp=95bec6887c488deb7d270403a88b40903ce5fa94;hpb=d14782f26230244039bf38f6384a7a9106b0daed;p=samtools.git

diff --git a/sample.c b/sample.c
index 95bec68..830b9d1 100644
--- a/sample.c
+++ b/sample.c
@@ -9,6 +9,7 @@ bam_sample_t *bam_smpl_init(void)
 	bam_sample_t *s;
 	s = calloc(1, sizeof(bam_sample_t));
 	s->rg2smid = kh_init(sm);
+	s->sm2id = kh_init(sm);
 	return s;
 }
 
@@ -23,6 +24,7 @@ void bam_smpl_destroy(bam_sample_t *sm)
 	for (k = kh_begin(rg2smid); k != kh_end(rg2smid); ++k)
 		if (kh_exist(rg2smid, k)) free((char*)kh_key(rg2smid, k));
 	kh_destroy(sm, sm->rg2smid);
+	kh_destroy(sm, sm->sm2id);
 	free(sm);
 }
 
@@ -50,11 +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;
-	sm2id = kh_init(sm);
+	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;
@@ -68,14 +74,23 @@ 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);
-	kh_destroy(sm, sm2id);
 	return 0;
 }