BGI/SOAPsnp/SamCtrl.h

   1 /*
   2  ******************************************************************************
   3  *Copyright 2010
   4  *      BGI-SHENZHEN
   5  *All Rights Reserved
   6  *ATHUOR : Bill Tang
   7  *CREATE DATE : 2010-7-29
   8  *CLASS NAME: SamCtrl
   9  *FUNCTION : a class that can control sam/bam format file. It is convenient to control sam/bam
  10  *                      format file like open, read, write, close and so on.
  11  *FILE NAME : SamCtrl.h
  12  *UPDATE DATE : 2010-7-30
  13  *UPDATE BY : Bill Tang
  14  *******************************************************************************
  15  */
  16
  17 #pragma once
  18
  19 #include <cmath>
  20 #include <string>
  21 #include "sam/bam.h"
  22 #include "sam/faidx.h"
  23 #include "sam/knetfile.h"
  24 #include "sam/sam.h"
  25 #include "sam/sam_view.h"
  26 #include "sam/xcurses.h"
  27 #include "sam/zlib.h"
  28 #include "sam/bgzf.h"
  29 #include "sam/glf.h"
  30 #include "sam/kstring.h"
  31 #include "sam/razf.h"
  32 #include "sam/sam_header.h"
  33 #include "sam/zconf.h"
  34
  35 class SamCtrl
  36 {
  37 private:
  38         std::string m_in_path; // the sam/bam in file's path.
  39         std::string m_out_path; // the sam/bam out file's path.
  40         samfile_t *m_in; // sam/bam file handler, use as reading.
  41         samfile_t *m_out; // sam/bam file handler, use as writing.
  42         std::string m_in_mode; // reading mode
  43         std::string m_out_mode; // wrinting mode
  44         char *m_fn_list; // sam/bam file list.
  45         char *m_s; // an tmp varible
  46         bam1_t *m_b; // a bam constructor.
  47 public:
  48         SamCtrl();
  49         ~SamCtrl(void);
  50
  51         bool open(const char *path, const char *mode);
  52         void close();
  53         int readline(std::string &line);
  54         bool isOpened();
  55 };
  56