X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mgclustercommand.cpp;h=9a1ac215388e09e6477fffa034e0542c38c208b1;hb=ccaad73f103d8f105264d65491ce19e5df80477d;hp=b92927b1d3d51c0505fbcadd14231eade34b78e5;hpb=a8367302932de9be5434e77f6e5829d7609e2aec;p=mothur.git

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index b92927b..9a1ac21 100644
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -500,13 +500,16 @@ ListVector* MGClusterCommand::mergeOPFs(map<string, int> binInfo, float dist){
 					float overlapDistance;
 					inOverlap >> firstName >> secondName >> overlapDistance; gobble(inOverlap);
 					
-					map<string,int>::iterator itA = nameMap->find(firstName);
-					map<string,int>::iterator itB = nameMap->find(secondName);
-					if(itA == nameMap->end()){  cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1);  }
-					if(itB == nameMap->end()){  cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);  }
+					//commented out because we check this in readblast already
+					//map<string,int>::iterator itA = nameMap->find(firstName);
+					//map<string,int>::iterator itB = nameMap->find(secondName);
+					//if(itA == nameMap->end()){  cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1);  }
+					//if(itB == nameMap->end()){  cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);  }
 					
-					overlapNode.seq1 = itA->second;
-					overlapNode.seq2 = itB->second;
+					//overlapNode.seq1 = itA->second;
+					//overlapNode.seq2 = itB->second;
+					overlapNode.seq1 = nameMap->get(firstName);
+					overlapNode.seq2 = nameMap->get(secondName);
 					overlapNode.dist = overlapDistance;
 				}else { inOverlap.close(); break; }
 			} 
@@ -517,14 +520,17 @@ ListVector* MGClusterCommand::mergeOPFs(map<string, int> binInfo, float dist){
 				string name2 = nameMap->get(overlapNode.seq2);
 			
 				//use binInfo to find out if they are already in the same bin
-				map<string, int>::iterator itBin1 = binInfo.find(name1);
-				map<string, int>::iterator itBin2 = binInfo.find(name2);
+				//map<string, int>::iterator itBin1 = binInfo.find(name1);
+				//map<string, int>::iterator itBin2 = binInfo.find(name2);
 				
-				if(itBin1 == binInfo.end()){  cerr << "AAError: Sequence '" << name1 << "' does not have any bin info.\n"; exit(1);  }
-				if(itBin2 == binInfo.end()){  cerr << "ABError: Sequence '" << name2 << "' does not have any bin info.\n"; exit(1);  }
+				//if(itBin1 == binInfo.end()){  cerr << "AAError: Sequence '" << name1 << "' does not have any bin info.\n"; exit(1);  }
+				//if(itBin2 == binInfo.end()){  cerr << "ABError: Sequence '" << name2 << "' does not have any bin info.\n"; exit(1);  }
 
-				int binKeep = itBin1->second;
-				int binRemove = itBin2->second;
+				//int binKeep = itBin1->second;
+				//int binRemove = itBin2->second;
+				
+				int binKeep = binInfo[name1];
+				int binRemove = binInfo[name2];
 			
 				//if not merge bins and update binInfo
 				if(binKeep != binRemove) {