X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sam.h;h=0b87194e05670ba287c9debe6e22c4d79a54e353;hb=8928103fafd05b9b555f9ae1710031666725867a;hp=f06439b78a9510ea3e5e684af55ea7c64c9d77a6;hpb=6f6733c7551a2f4697c46acb4a516fa04bba3e40;p=samtools.git

diff --git a/sam.h b/sam.h
index f06439b..0b87194 100644
--- a/sam.h
+++ b/sam.h
@@ -51,7 +51,8 @@ extern "C" {
 	  @param aux auxiliary data; if mode[0]=='w', aux points to
 	  bam_header_t; if strcmp(mode, "rb")!=0 and @SQ header lines in SAM
 	  are absent, aux points the file name of the list of the reference;
-	  aux is not used otherwise.
+	  aux is not used otherwise. If @SQ header lines are present in SAM,
+	  aux is not used, either.
 
 	  @return       SAM/BAM file handler
 	 */
@@ -88,6 +89,8 @@ extern "C" {
 	 */
 	int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *data);
 
+	char *samfaipath(const char *fn_ref);
+
 #ifdef __cplusplus
 }
 #endif