From: pschloss <pschloss>
Date: Wed, 9 Feb 2011 15:25:04 +0000 (+0000)
Subject: mods to shhhercommand and seqerrorcommand
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=10891fa4322cd356285cd8058f3b399bc766c5ea

mods to shhhercommand and seqerrorcommand
---

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 00f7862..8879478 100644
--- 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 e2f2636..7768fa7 100644
--- 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){