Revert one of my earlier changes - Heng was right, CIGAR P not sensible in a padded...

[samtools.git] / sam.h

diff --git a/sam.h b/sam.h
index f06439b78a9510ea3e5e684af55ea7c64c9d77a6..049550161628948dc7a0f085ff936d07742d4485 100644 (file)
--- 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 +89,9 @@ extern "C" {
         */
        int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *data);
 
+       char *samfaipath(const char *fn_ref);
+       int samthreads(samfile_t *fp, int n_threads, int n_sub_blks);
+
 #ifdef __cplusplus
 }
 #endif