X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sam.h;h=049550161628948dc7a0f085ff936d07742d4485;hb=70c740facc966321754c6bfcc6d61ea056480638;hp=b8a0064cdec6472d366ae35fb4e0a276aa17c358;hpb=941542dfbedf4ba4850d3c1d6b96981234fd6560;p=samtools.git

diff --git a/sam.h b/sam.h
index b8a0064..0495501 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, 2 for reading and bit 3 for is_hex
+  @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?)(x?)/: 'r' for reading, 'w'
-	  for writing, 'b' for BAM I/O, 'u' for uncompressed BAM output, 'h'
-	  for outputing header in SAM and 'x' for HEX flag. If 'b' present,
-	  it must immediately follow 'r' or 'w'. Valid modes are "r", "w",
-	  "wh", "wx", "whx", "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
 	  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 +89,9 @@ 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