BGI/SOAPsnp/Files.cpp

   1 /*
   2  ******************************************************************************
   3  *Copyright 2010
   4  *      BGI-SHENZHEN
   5  *All Rights Reserved
   6  *ATHUOR : Bill Tang
   7  *CREATE DATE : 2010-9-15
   8  *UPDATE DATE : 2010-9-15
   9  *UPDATE BY :   Zhou Guyue
  10  *******************************************************************************
  11  */
  12
  13
  14
  15 #include "soap_snp.h"
  16 #include <cassert>
  17
  18 /**
  19  * DATE: 2010-9-15
  20  * FUNCTION: open sfs file
  21  * PARAMETER: outfiles : outfile name.
  22                           writeFr : whether writer frequence file.
  23                           doBay : whether do Bay.
  24                           doJoint : whether do Joint
  25  * RETURN:       OPENSFS_ERROR:if can not open file  ,OPENSFS_SUCC : if can open file.
  26  */
  27 int Files::OpenSfsfile(const string outfiles, const int writeFr, const int doBay, const int doJoint)
  28 {
  29          //generete the output filenames
  30         if(!outfiles.c_str())
  31         {
  32                 printf("Must supply -outfiles (-fai)\n");
  33                 return OPENSFS_ERROR;
  34         }
  35
  36         fSFSall = outfiles + ".sfs";
  37         fFreq = outfiles + ".frq";
  38         fJoint = outfiles + ".bjoint";
  39
  40     //open the persite FILE streams
  41         if(writeFr)
  42         {
  43                 //freqfile.clear();
  44                 //freqfile.open(fFreq.c_str());
  45                 freqfile= getFILE(fFreq.c_str(),"w");
  46         }
  47         if(doBay)
  48         {
  49                 //sfsfile.clear();
  50                 //sfsfile.open(fSFSall.c_str());
  51                 sfsfile = getFILE(fSFSall.c_str(),"w");
  52                 //sfsfile-open(fSFSall.c_str());
  53         }
  54         if(doJoint)
  55         {
  56                 //jointSfsfile.clear();
  57                 //jointSfsfile.open(fJoint.c_str(), ios::binary);
  58                 jointSfsfile = getFILE(fJoint.c_str(),"w");
  59         }
  60         if ((writeFr && !freqfile) || (doBay && !sfsfile) || (doJoint && !jointSfsfile))
  61         {
  62                 cerr << "\topen sfs file failed!" << endl;
  63                 return OPENSFS_ERROR;
  64         }
  65         return OPENSFS_SUCC;
  66
  67 }
  68
  69  /**
  70  * DATE: 2010-9-15
  71  * FUNCTION: get file in mode
  72  * PARAMETER: fname : file name , mode : write.
  73  * RETURN:       FILE .
  74  */
  75 FILE* Files::getFILE(const char*fname,const char* mode)
  76 {
  77         FILE *fp;
  78         if(NULL == (fp = fopen(fname, mode)))
  79         {
  80                 fprintf(stderr,"\t->Error opening FILE handle for file:%s exiting\n",fname);
  81                 exit(0);
  82         }
  83         return fp;
  84 }