another attempt to fix sffinfo

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 7511a2e613bb08912044ad3c044cf3a6a8f91c40..f8ba25b5fabd1b8485065a548e47911cb0c8c1e3 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -405,12 +405,12 @@ int SffInfoCommand::readHeader(ifstream& in, Header& header){
                        char buffer4 [2];
                        in.read(buffer4, 2);
                        header.clipQualLeft =  be_int2(*(unsigned short *)(&buffer4));
+                       header.clipQualLeft = 5;
                        
                        //read clip qual right
                        char buffer5 [2];
                        in.read(buffer5, 2);
                        header.clipQualRight =  be_int2(*(unsigned short *)(&buffer5));
-                       if(header.clipQualRight == 0){  header.clipQualRight = header.numBases; }
                        
                        //read clipAdapterLeft
                        char buffer6 [2];
@@ -586,11 +586,17 @@ int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& head
                string seq = read.bases;
                
                if (trim) {
-                       seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft+1));
+                       if(header.clipQualRight != 0){
+                               seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
+                       }
+                       else {
+                               seq = seq.substr(header.clipQualLeft-1);
+                       }
                }else{
                        //if you wanted the sfftxt then you already converted the bases to the right case
                        if (!sfftxt) {
                                //make the bases you want to clip lowercase and the bases you want to keep upper case
+                               if(header.clipQualRight == 0){  header.clipQualRight = seq.length();    }
                                for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]);  }
                                for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++)  {   seq[i] = toupper(seq[i]);  }
                                for (int i = (header.clipQualRight-1); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }
@@ -613,8 +619,14 @@ int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& heade
        try {
                
                if (trim) {
-                       out << ">" << header.name << " length=" << (header.clipQualRight-header.clipQualLeft+1) << endl;
-                       for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   out << read.qualScores[i] << '\t';  }
+                       if(header.clipQualRight != 0){
+                               out << ">" << header.name << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
+                               for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   out << read.qualScores[i] << '\t'; }
+                       }
+                       else{
+                               out << ">" << header.name << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
+                               for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';   }                       
+                       }
                }else{
                        out << ">" << header.name << " length=" << read.qualScores.size() << endl;
                        for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }