mods to shhhercommand and seqerrorcommand

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 00f78626b6270455f5a8f35464923fe72e9ff527..88794788a0472743665838721bb28b9b761f1765 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -505,7 +505,7 @@ Compare SeqErrorCommand::getErrors(Sequence query, Sequence reference){
                                if(started == 1){       break;  }
                        }
                        else if(q[i] != '.' && r[i] == '.'){            //      query extends beyond reference
-                               m->mothurOut("Warning: " + toString(query.getName()) + " extend beyond " + toString(reference.getName()) + ".  Ignoring the extra bases in the query\n");
+//                             m->mothurOut("Warning: " + toString(query.getName()) + " extend beyond " + toString(reference.getName()) + ".  Ignoring the extra bases in the query\n");
                                if(started == 1){       break;  }
                        }
                        else if(q[i] == '.' && r[i] == '.'){            //      both are missing data

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index e2f2636e491294a7e260e34340cef1e4e8273d40..7768fa74f1d58fa4f5e15f1031c6046a5bccb58f 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -994,10 +994,10 @@ void ShhherCommand::flowDistParentFork(string distFileName, int startSeq, int st
                                float flowDistance = calcPairwiseDist(mapUniqueToSeq[i], mapUniqueToSeq[j]);
 
                                if(flowDistance < 1e-6){
-                                       outStream << seqNameVector[mapUniqueToSeq[i]] << '\t' << seqNameVector[mapUniqueToSeq[j]] << '\t' << 0.000000 << endl;
+                                       outStream << mapUniqueToSeq[i] << '\t' << mapUniqueToSeq[j] << '\t' << 0.000000 << endl;
                                }
                                else if(flowDistance <= cutoff){
-                                       outStream << seqNameVector[mapUniqueToSeq[i]] << '\t' << seqNameVector[mapUniqueToSeq[j]] << '\t' << flowDistance << endl;
+                                       outStream << mapUniqueToSeq[i] << '\t' << mapUniqueToSeq[j] << '\t' << flowDistance << endl;
                                }
                        }
                        if(i % 100 == 0){