X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=sam.h;h=0b87194e05670ba287c9debe6e22c4d79a54e353;hp=970cf2daee7ca49a95280bcf1431ae35ba8f223f;hb=4a17fa7e1f91b2fe04ad334a63fc2b0d5e859d8a;hpb=b27e00385f41769d03a8cca4dbd71275fc9fa906

diff --git a/sam.h b/sam.h
index 970cf2d..0b87194 100644
--- a/sam.h
+++ b/sam.h
@@ -15,7 +15,7 @@
 
 /*! @typedef
   @abstract SAM/BAM file handler
-  @field  type    type of the handler; bit 1 for BAM and bit 2 for reading
+  @field  type    type of the handler; bit 1 for BAM, 2 for reading and bit 3-4 for flag format
   @field  bam   BAM file handler; valid if (type&1) == 1
   @field  tamr  SAM file handler for reading; valid if type == 2
   @field  tamw  SAM file handler for writing; valid if type == 0
@@ -41,16 +41,18 @@ extern "C" {
 	  @param fn SAM/BAM file name; "-" is recognized as stdin (for
 	  reading) or stdout (for writing).
 
-	  @param mode open mode /[rw](b?)(u?)(h?)/: 'r' for reading, 'w' for
-	  writing, 'b' for BAM I/O, 'u' for uncompressed BAM output and 'h'
-	  for outputing header in SAM. If 'b' present, it must immediately
-	  follow 'r' or 'w'. Valid modes are "r", "w", "wh", "rb", "wb" and
-	  "wbu" exclusively.
+	  @param mode open mode /[rw](b?)(u?)(h?)([xX]?)/: 'r' for reading,
+	  'w' for writing, 'b' for BAM I/O, 'u' for uncompressed BAM output,
+	  'h' for outputing header in SAM, 'x' for HEX flag and 'X' for
+	  string flag. If 'b' present, it must immediately follow 'r' or
+	  'w'. Valid modes are "r", "w", "wh", "wx", "whx", "wX", "whX",
+	  "rb", "wb" and "wbu" exclusively.
 
 	  @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
+	  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
 	 */
@@ -87,6 +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