X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sam.h;h=049550161628948dc7a0f085ff936d07742d4485;hb=607d7a0ab79152be4153fa09861cfa889488f2c7;hp=082fe96b24913a2172b9b5b89036cb8fd91f1f0f;hpb=9360df156b23158232dca10ffdb8a8ffdcaf0930;p=samtools.git

diff --git a/sam.h b/sam.h
index 082fe96..0495501 100644
--- a/sam.h
+++ b/sam.h
@@ -3,6 +3,24 @@
 
 #include "bam.h"
 
+/*!
+  @header
+
+  This file provides higher level of I/O routines and unifies the APIs
+  for SAM and BAM formats. These APIs are more convenient and
+  recommended.
+
+  @copyright Genome Research Ltd.
+ */
+
+/*! @typedef
+  @abstract SAM/BAM file handler
+  @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
+  @field  header  header struct
+ */
 typedef struct {
 	int type;
 	union {
@@ -17,12 +35,62 @@ typedef struct {
 extern "C" {
 #endif
 
-	// mode can be: r/w/rb/wb. On writing, aux points to bam_header_t; on reading, aux points to the name of fn_list for SAM
+	/*!
+	  @abstract     Open a SAM/BAM file
+
+	  @param fn SAM/BAM file name; "-" is recognized as stdin (for
+	  reading) or stdout (for writing).
+
+	  @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. If @SQ header lines are present in SAM,
+	  aux is not used, either.
+
+	  @return       SAM/BAM file handler
+	 */
 	samfile_t *samopen(const char *fn, const char *mode, const void *aux);
+
+	/*!
+	  @abstract     Close a SAM/BAM handler
+	  @param  fp    file handler to be closed
+	 */
 	void samclose(samfile_t *fp);
+
+	/*!
+	  @abstract     Read one alignment
+	  @param  fp    file handler
+	  @param  b     alignment
+	  @return       bytes read
+	 */
 	int samread(samfile_t *fp, bam1_t *b);
+
+	/*!
+	  @abstract     Write one alignment
+	  @param  fp    file handler
+	  @param  b     alignment
+	  @return       bytes written
+	 */
 	int samwrite(samfile_t *fp, const bam1_t *b);
-	int sampileup(samfile_t *fp, int mask, int min_mapQ, bam_pileup_f func, void *func_data);
+
+	/*!
+	  @abstract     Get the pileup for a whole alignment file
+	  @param  fp    file handler
+	  @param  mask  mask transferred to bam_plbuf_set_mask()
+	  @param  func  user defined function called in the pileup process
+	  #param  data  user provided data for func()
+	 */
+	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
 }