X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fsample.c.pysam.c;h=dc8e627ec5382382d77ac3860c401d88253cf3af;hp=5f3d655e21a969e8d0c43fb9f122e1bfab75d11d;hb=e1756c41e7a1d7cc01fb95e42df9dd04da2d2991;hpb=ca46ef4ba4a883c57cea62d5bf1bc021f1185109

diff --git a/samtools/sample.c.pysam.c b/samtools/sample.c.pysam.c
index 5f3d655..dc8e627 100644
--- a/samtools/sample.c.pysam.c
+++ b/samtools/sample.c.pysam.c
@@ -54,15 +54,10 @@ 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, first_sm;
+	kstring_t buf;
 	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;
@@ -76,21 +71,12 @@ 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;