match(m), // This is the score to award for two nucleotides matching (match >= 0)
mismatch(mm) // This is the penalty to assess for a mismatch (mismatch <= 0)
{
+ globaldata = GlobalData::getInstance();
+ path = globaldata->argv;
+ path = path.substr(0, (path.find_last_of('m')));
+
gapOpen = abs(go); // This is the penalty to assess for opening a gap (gapOpen >= 0)
gapExtend = abs(ge); // This is the penalty to assess for extending a gap (gapExtend >= 0)
// The blastCommand assumes that we have DNA sequences (blastn) and that they are fairly similar (-e 0.001) and
// that we don't want to apply any kind of complexity filtering (-F F)
- string blastCommand = "~/Pipeline/src/cpp/production/blast/bin/bl2seq -p blastn -i " + candidateFileName + " -j " + templateFileName + " -e 0.0001 -F F -o " + blastFileName + " -W 11";
+ string blastCommand = path + "blast/bin/bl2seq -p blastn -i " + candidateFileName + " -j " + templateFileName + " -e 0.0001 -F F -o " + blastFileName + " -W 11";
blastCommand += " -r " + toString(match) + " -q " + toString(mismatch);
blastCommand += " -G " + toString(gapOpen) + " -E " + toString(gapExtend);