fixed trim.seqs bug with qtrim parameter and added num=1 special case to database...

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index d5df4730c9f118966de5f3514b4ec276faffce05..2dc07794be5abb2f239e4b228c3aacbf51c51b6e 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -556,16 +556,16 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 
                                
                                if(qFileName != ""){
+                                       int origLength = currSeq.getNumBases();
                                        
                                        if(qThreshold != 0)                     {       success = currQual.stripQualThreshold(currSeq, qThreshold);                     }
                                        else if(qAverage != 0)          {       success = currQual.cullQualAverage(currSeq, qAverage);                          }
                                        else if(qRollAverage != 0)      {       success = currQual.stripQualRollingAverage(currSeq, qRollAverage);      }
                                        else if(qWindowAverage != 0){   success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage);   }
                                        else                                            {       success = 1;                            }
-
-//                                     if (qtrim == 1 && (origSeq.length() != currSeq.getUnaligned().length())) { 
-//                                             success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
-//                                     }
+                                       
+                                       //you don't want to trim, if it fails above then scrap it
+                                       if ((!qtrim) && (origLength != currSeq.getNumBases())) { success = 0; }
                                        
                                        if(!success)                            {       trashCode += 'q';       }
                                }