From b188ebcd53973ed3084aff5d5e2ad4a3475dd17e Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Sat, 24 Oct 2009 04:45:12 +0000
Subject: [PATCH]  * BUGGY VERSION  * improved the interface a bit  * bug
 unfixed

---
 bam.c        | 6 ++++--
 bam.h        | 2 +-
 bam_import.c | 7 -------
 sam.c        | 1 -
 4 files changed, 5 insertions(+), 11 deletions(-)

diff --git a/bam.c b/bam.c
index 8b51756..2d0f7f4 100644
--- a/bam.c
+++ b/bam.c
@@ -292,9 +292,11 @@ void bam_view1(const bam_header_t *header, const bam1_t *b)
 	free(s);
 }
 
-const char *bam_get_library(const bam_header_t *header, const bam1_t *b)
+const char *bam_get_library(bam_header_t *h, const bam1_t *b)
 {
 	const uint8_t *rg;
+	if (h->dict == 0) h->dict = sam_header_parse2(h->text);
+	if (h->rg2lib) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB");
 	rg = bam_aux_get(b, "RG");
-	return (rg == 0)? 0 : sam_tbl_get(header->rg2lib, (const char*)(rg + 1));
+	return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1));
 }
diff --git a/bam.h b/bam.h
index 4d30dcc..291b303 100644
--- a/bam.h
+++ b/bam.h
@@ -438,7 +438,7 @@ extern "C" {
 
 	char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of);
 
-	const char *bam_get_library(const bam_header_t *header, const bam1_t *b);
+	const char *bam_get_library(bam_header_t *header, const bam1_t *b);
 
 	/*! @typedef
 	  @abstract Structure for one alignment covering the pileup position.
diff --git a/bam_import.c b/bam_import.c
index 2b4fb7e..34cc776 100644
--- a/bam_import.c
+++ b/bam_import.c
@@ -171,13 +171,6 @@ static inline void append_text(bam_header_t *header, kstring_t *str)
 	header->text[header->l_text] = 0;
 }
 
-int sam_header_parse_rg(bam_header_t *h)
-{
-	if (h->dict == 0) h->dict = sam_header_parse2(h->text);
-	if (h->rg2lib) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB");
-	return sam_tbl_size(h->rg2lib);
-}
-
 int sam_header_parse(bam_header_t *h)
 {
 	char **tmp;
diff --git a/sam.c b/sam.c
index 07524c0..f88ad53 100644
--- a/sam.c
+++ b/sam.c
@@ -62,7 +62,6 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
 					fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
 			} else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
 		}
-		sam_header_parse_rg(fp->header);
 	} else if (mode[0] == 'w') { // write
 		fp->header = bam_header_dup((const bam_header_t*)aux);
 		if (mode[1] == 'b') { // binary
-- 
2.39.2