Imported Upstream version 0.5

[pysam.git] / samtools / sample.c.pysam.c

diff --git a/samtools/sample.c.pysam.c b/samtools/sample.c.pysam.c
index 5f3d655e21a969e8d0c43fb9f122e1bfab75d11d..dc8e627ec5382382d77ac3860c401d88253cf3af 100644 (file)
--- 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;