another pds fix to sffinfo

[mothur.git] / sffinfocommand.cpp

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 8c0e473a87e86453c8721b0f5c5b5bde947b703b..7511a2e613bb08912044ad3c044cf3a6a8f91c40 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -410,6 +410,7 @@ int SffInfoCommand::readHeader(ifstream& in, Header& header){
                        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];
@@ -584,7 +585,6 @@ 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));
                }else{