BGI/SOAPsnp/SamCtrl.cpp

   1 /*
   2  *****************************************************************************
   3  *Copyright 2010
   4  *      BGI-SHENZHEN
   5  *All Rights Reserved
   6  *ATHUOR : Bill Tang
   7  *CREATE DATE : 2010-7-29
   8  *FUNCTION : definition of class SamCtrl
   9  *FILE NAME : SamCtrl.cpp
  10  *UPDATE DATE : 2010-8-1
  11  *UPDATE BY : Bill Tang
  12  *******************************************************************************
  13  */
  14
  15
  16 #include "SamCtrl.h"
  17
  18
  19 SamCtrl::SamCtrl()
  20 {
  21         m_out_path = "-";
  22         m_out_mode = "w";
  23         m_fn_list = 0;
  24         m_in = 0;
  25         m_out = 0;
  26         m_b = bam_init1(); // initialize m_b
  27
  28 }
  29
  30
  31 SamCtrl::~SamCtrl(void)
  32 {
  33         bam_destroy1(m_b);
  34         close();
  35 }
  36
  37 /**
  38  * DATE: 2010-7-29
  39  * FUNCTION: open sam/bam file in pattern mode.
  40  * PARAMETER: path: the file's path. mode: the pattern.
  41  * RETURN: successful: true. failed: flase.
  42  */
  43 bool SamCtrl::open(const char *path, const char *mode)
  44 {
  45         if (mode[0] == 'r') {
  46                 // judge if opened a file before
  47                 if (m_in != 0) {
  48                         return false;
  49                 }
  50
  51                 m_in_mode = mode;
  52                 m_in_path = path;
  53
  54                 // open sam/bam file
  55                 if ((m_in = samopen(m_in_path.c_str(), m_in_mode.c_str(), m_fn_list)) == 0)
  56                 {
  57                         return false;
  58                 }
  59
  60                 if (m_in->header == 0)
  61                 {
  62                         return false;
  63                 }
  64
  65                 if ((m_out = samopen(m_out_path.c_str(), m_out_mode.c_str(), m_in->header)) == 0)
  66                 {
  67                         return false;
  68                 }
  69                 return true;
  70         }
  71         return false;
  72 }
  73
  74 /**
  75  * DATE: 2010-7-29
  76  * FUNCTION: read a line from sam/bam file.
  77  * PARAMETER: line: the read data will stored in this varible.
  78  * RETURN: the line size when read successful. -1 when read failed
  79  */
  80 int SamCtrl::readline(std::string &line)
  81 {
  82         if (m_in == 0)
  83         {
  84                 return -1;
  85         }
  86
  87         int ret = 0;
  88         // begin to read
  89         while ((ret = samread(m_in, m_b)) >= 0)
  90         {
  91                 // when read failed continue
  92                 if (__g_skip_aln(m_in->header, m_b))
  93                 {
  94                         continue;
  95         }
  96
  97                 m_s = bam_format1_core(m_out->header, m_b, m_out->type>>2&3); // read the buffer
  98                 line = m_s; // store into the line
  99                 free(m_s);
 100                 return line.size();
 101         }
 102         return -1;
 103 }
 104
 105 /**
 106  * DATE: 2010-7-29
 107  * FUNCTION: close the sam/bam file
 108  * PARAMETER: void
 109  * RETURN: void
 110  */
 111 void SamCtrl::close()
 112 {
 113         if (m_fn_list != 0)
 114                 delete m_fn_list;
 115         if (m_in != 0)
 116                 samclose(m_in);
 117         if (m_out != 0)
 118                 samclose(m_out);
 119         m_in = 0;
 120         m_out = 0;
 121         m_fn_list = 0;
 122 }
 123
 124 /**
 125  * DATE: 2010-7-29
 126  * FUNCTION: judge if the file is opened successful
 127  * PARAMETER: void
 128  * RETURN: true if successful else false if failed
 129  */
 130 bool SamCtrl::isOpened()
 131 {
 132         return !(m_in == 0);
 133 }