fixed blast code path problem

[mothur.git] / blastalign.cpp

diff --git a/blastalign.cpp b/blastalign.cpp
index 0a1350fac0c7fa655d5d04585156c28445c4d0d5..a4773138bd6f8102acaea659291fa675ea25a6fc 100644 (file)
--- a/blastalign.cpp
+++ b/blastalign.cpp
@@ -23,6 +23,10 @@ BlastAlignment::BlastAlignment(float go, float ge, float m, float mm) :
                        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)
                
@@ -54,7 +58,7 @@ void BlastAlignment::align(string seqA, string seqB){ //Use blastn to align the
        
        //      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);