fixed a trimming bug in sffinfo which occurs when the right trim point is smaller...

[mothur.git] / sffinfocommand.cpp

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index f8ba25b5fabd1b8485065a548e47911cb0c8c1e3..4e53f69cb3e7dd51c3d4b30c10a09d76339b6f2c 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -405,7 +405,7 @@ int SffInfoCommand::readHeader(ifstream& in, Header& header){
                        char buffer4 [2];
                        in.read(buffer4, 2);
                        header.clipQualLeft =  be_int2(*(unsigned short *)(&buffer4));
-                       header.clipQualLeft = 5;
+                       header.clipQualLeft = 5; 
                        
                        //read clip qual right
                        char buffer5 [2];
@@ -562,6 +562,7 @@ int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read, Header& hea
                for (int i = 0; i < read.flowIndex.size(); i++) {  sum +=  read.flowIndex[i];  out << sum << '\t'; }
                
                //make the bases you want to clip lowercase and the bases you want to keep upper case
+               if(header.clipQualRight == 0){  header.clipQualRight = read.bases.length();     }
                for (int i = 0; i < (header.clipQualLeft-1); i++) { read.bases[i] = tolower(read.bases[i]); }
                for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   read.bases[i] = toupper(read.bases[i]);  }
                for (int i = (header.clipQualRight-1); i < read.bases.length(); i++) {   read.bases[i] = tolower(read.bases[i]);  }
@@ -586,7 +587,10 @@ int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& head
                string seq = read.bases;
                
                if (trim) {
-                       if(header.clipQualRight != 0){
+                       if(header.clipQualRight < header.clipQualLeft){
+                               seq = "NNNN";
+                       }
+                       else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
                                seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
                        }
                        else {
@@ -619,7 +623,10 @@ int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& heade
        try {
                
                if (trim) {
-                       if(header.clipQualRight != 0){
+                       if(header.clipQualRight < header.clipQualLeft){
+                               out << "0\t0\t0\t0";
+                       }
+                       else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 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'; }
                        }