* samtools-0.1.5-12 (r415)

[samtools.git] / sam.h

diff --git a/sam.h b/sam.h
index 86b757616e44b1e4de8ddd2da383534a805fe246..b8a0064cdec6472d366ae35fb4e0a276aa17c358 100644 (file)
--- 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 for is_hex
   @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
@@ -41,11 +41,11 @@ 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?)(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 aux auxiliary data; if mode[0]=='w', aux points to
          bam_header_t; if strcmp(mode, "rb")!=0 and @SQ header lines in SAM