ebwt.cpp

   1 /*
   2  * ebwt.cpp
   3  *
   4  *  Created on: Sep 23, 2009
   5  *      Author: Ben Langmead
   6  */
   7
   8 #include <string>
   9 #include <stdexcept>
  10 #include <iostream>
  11 #include <fstream>
  12 #include <stdlib.h>
  13
  14 using namespace std;
  15
  16 /**
  17  * Try to find the Bowtie index specified by the user.  First try the
  18  * exact path given by the user.  Then try the user-provided string
  19  * appended onto the path of the "indexes" subdirectory below this
  20  * executable, then try the provided string appended onto
  21  * "$BOWTIE_INDEXES/".
  22  */
  23 string adjustEbwtBase(const string& cmdline,
  24                                           const string& ebwtFileBase,
  25                                           bool verbose = false)
  26 {
  27         string str = ebwtFileBase;
  28         ifstream in;
  29         if(verbose) cout << "Trying " << str << endl;
  30         in.open((str + ".1.ebwt").c_str(), ios_base::in | ios::binary);
  31         if(!in.is_open()) {
  32                 if(verbose) cout << "  didn't work" << endl;
  33                 in.close();
  34                 str = cmdline;
  35                 size_t st = str.find_last_of("/\\");
  36                 if(st != string::npos) {
  37                         str.erase(st);
  38                         str += "/indexes/";
  39                 } else {
  40                         str = "indexes/";
  41                 }
  42                 str += ebwtFileBase;
  43                 if(verbose) cout << "Trying " << str << endl;
  44                 in.open((str + ".1.ebwt").c_str(), ios_base::in | ios::binary);
  45                 if(!in.is_open()) {
  46                         if(verbose) cout << "  didn't work" << endl;
  47                         in.close();
  48                         if(getenv("BOWTIE_INDEXES") != NULL) {
  49                                 str = string(getenv("BOWTIE_INDEXES")) + "/" + ebwtFileBase;
  50                                 if(verbose) cout << "Trying " << str << endl;
  51                                 in.open((str + ".1.ebwt").c_str(), ios_base::in | ios::binary);
  52                                 if(!in.is_open()) {
  53                                         if(verbose) cout << "  didn't work" << endl;
  54                                         in.close();
  55                                 } else {
  56                                         if(verbose) cout << "  worked" << endl;
  57                                 }
  58                         }
  59                 }
  60         }
  61         if(!in.is_open()) {
  62                 cerr << "Could not locate a Bowtie index corresponding to basename \"" << ebwtFileBase << "\"" << endl;
  63                 throw 1;
  64         }
  65         return str;
  66 }