BGI/SOAPdenovo2/sparsePregraph/inc/sam.h

   1 #ifndef BAM_SAM_H
   2 #define BAM_SAM_H
   3
   4 #include "bam.h"
   5
   6 /*!
   7   @header
   8
   9   This file provides higher level of I/O routines and unifies the APIs
  10   for SAM and BAM formats. These APIs are more convenient and
  11   recommended.
  12
  13   @copyright Genome Research Ltd.
  14  */
  15
  16 /*! @typedef
  17   @abstract SAM/BAM file handler
  18   @field  type    type of the handler; bit 1 for BAM, 2 for reading and bit 3-4 for flag format
  19   @field  bam   BAM file handler; valid if (type&1) == 1
  20   @field  tamr  SAM file handler for reading; valid if type == 2
  21   @field  tamw  SAM file handler for writing; valid if type == 0
  22   @field  header  header struct
  23  */
  24 typedef struct
  25 {
  26         int type;
  27         union
  28         {
  29                 tamFile tamr;
  30                 bamFile bam;
  31                 FILE * tamw;
  32         } x;
  33         bam_header_t * header;
  34 } samfile_t;
  35
  36 #ifdef __cplusplus
  37 extern "C" {
  38 #endif
  39
  40         /*!
  41           @abstract     Open a SAM/BAM file
  42
  43           @param fn SAM/BAM file name; "-" is recognized as stdin (for
  44           reading) or stdout (for writing).
  45
  46           @param mode open mode /[rw](b?)(u?)(h?)([xX]?)/: 'r' for reading,
  47           'w' for writing, 'b' for BAM I/O, 'u' for uncompressed BAM output,
  48           'h' for outputing header in SAM, 'x' for HEX flag and 'X' for
  49           string flag. If 'b' present, it must immediately follow 'r' or
  50           'w'. Valid modes are "r", "w", "wh", "wx", "whx", "wX", "whX",
  51           "rb", "wb" and "wbu" exclusively.
  52
  53           @param aux auxiliary data; if mode[0]=='w', aux points to
  54           bam_header_t; if strcmp(mode, "rb")!=0 and @SQ header lines in SAM
  55           are absent, aux points the file name of the list of the reference;
  56           aux is not used otherwise. If @SQ header lines are present in SAM,
  57           aux is not used, either.
  58
  59           @return       SAM/BAM file handler
  60          */
  61         samfile_t * samopen ( const char * fn, const char * mode, const void * aux );
  62
  63         /*!
  64           @abstract     Close a SAM/BAM handler
  65           @param  fp    file handler to be closed
  66          */
  67         void samclose ( samfile_t * fp );
  68
  69         /*!
  70           @abstract     Read one alignment
  71           @param  fp    file handler
  72           @param  b     alignment
  73           @return       bytes read
  74          */
  75         int samread ( samfile_t * fp, bam1_t * b );
  76
  77         /*!
  78           @abstract     Write one alignment
  79           @param  fp    file handler
  80           @param  b     alignment
  81           @return       bytes written
  82          */
  83         int samwrite ( samfile_t * fp, const bam1_t * b );
  84
  85         /*!
  86           @abstract     Get the pileup for a whole alignment file
  87           @param  fp    file handler
  88           @param  mask  mask transferred to bam_plbuf_set_mask()
  89           @param  func  user defined function called in the pileup process
  90           #param  data  user provided data for func()
  91          */
  92         int sampileup ( samfile_t * fp, int mask, bam_pileup_f func, void * data );
  93
  94         char * samfaipath ( const char * fn_ref );
  95
  96 #ifdef __cplusplus
  97 }
  98 #endif
  99
 100 #endif