added adjustDots function to pcr.seqs, keeps sequences aligned in case where primers...

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 2c88bef2d036e798a0e84a85d0af1120c3fdd6df..81b9111b17dd8bba332ad8a8267cc12bf16e235a 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -422,7 +422,7 @@ int TrimSeqsCommand::execute(){
                
                if (countfile != "") {
             CountTable ct;
-            ct.readTable(countfile);
+            ct.readTable(countfile, true);
             nameCount = ct.getNameMap();
                        outputNames.push_back(trimCountFile);
                        outputNames.push_back(scrapCountFile);
@@ -540,7 +540,7 @@ int TrimSeqsCommand::execute(){
             
             if (countfile != "") { //create countfile with group info included
                 CountTable* ct = new CountTable();
-                ct->readTable(trimCountFile);
+                ct->readTable(trimCountFile, true);
                 map<string, int> justTrimmedNames = ct->getNameMap();
                 delete ct;
                 
@@ -1648,7 +1648,7 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
         if (hasPairedBarcodes || hasPrimer) {
             pairedOligos = true;
             if ((primers.size() != 0) || (barcodes.size() != 0) || (linker.size() != 0) || (spacer.size() != 0) || (revPrimer.size() != 0)) { m->control_pressed = true;  m->mothurOut("[ERROR]: cannot mix paired primers and barcodes with non paired or linkers and spacers, quitting."); m->mothurOutEndLine();  return 0; }
-        }
+        }else if (reorient) { m->mothurOut("[Warning]: cannot use checkorient without paired barcodes or primers, ignoring.\n"); m->mothurOutEndLine(); reorient = false; }
         
                if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0;   }