fixed project

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 5f7c9b2199d28960fe1b619a4df2394be3b352a6..7835b7598ae6ddcc76001788d44daf1faf17cfdd 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -999,13 +999,28 @@ bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
                int seqLength;  // = rawSequence.length();
                string name, temp, temp2;
                
-               qFile >> name >> temp;
+               qFile >> name;
+               
+               //get rest of line
+               temp = "";
+               while (!qFile.eof())    {       
+                       char c = qFile.get(); 
+                       if (c == 10 || c == 13){        break;  }       
+                       else { temp += c; }
+               } 
        
+               int pos = temp.find("length");
+               if (pos == temp.npos) { m->mothurOut("Cannot find length in qfile for " + seq.getName()); m->mothurOutEndLine();  seqLength = 0;  }
+               else {
+                       string tempLength = temp.substr(pos);
+                       istringstream iss (tempLength,istringstream::in);
+                       iss >> temp;
+               }
+               
                splitAtEquals(temp2, temp); //separates length=242, temp=length, temp2=242
                convert(temp, seqLength); //converts string to int
        
                if (name.length() != 0) {  if(name.substr(1) != seq.getName())  {       m->mothurOut("sequence name mismatch btwn fasta and qual file"); m->mothurOutEndLine(); }  } 
-               while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
                
                int score;
                int end = seqLength;