X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trimseqscommand.h;h=e280c8a1d4b50336f125dda5788d91d2af76c09a;hp=ba4e61411b8498820139e8ae2b1ed71cb37b0432;hb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;hpb=2c97dd48b8e27ee0a6a86c7a082f4c504c3357c6

diff --git a/trimseqscommand.h b/trimseqscommand.h
index ba4e614..e280c8a 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -413,11 +413,13 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
 							
 							outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl;
 							
+                            int numRedundants = 0;
 							if (pDataArray->nameFile != "") {
 								map<string, string>::iterator itName = pDataArray->nameMap.find(currSeq.getName());
 								if (itName != pDataArray->nameMap.end()) { 
 									vector<string> thisSeqsNames; 
 									pDataArray->m->splitAtChar(itName->second, thisSeqsNames, ',');
+                                    numRedundants = thisSeqsNames.size()-1; //we already include ourselves below
 									for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
 										outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
 									}
@@ -425,8 +427,8 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
 							}
 							
 							map<string, int>::iterator it = pDataArray->groupCounts.find(thisGroup);
-							if (it == pDataArray->groupCounts.end()) {	pDataArray->groupCounts[thisGroup] = 1; }
-							else { pDataArray->groupCounts[it->first]++; }
+							if (it == pDataArray->groupCounts.end()) {	pDataArray->groupCounts[thisGroup] = 1 + numRedundants; }
+							else { pDataArray->groupCounts[it->first] += (1 + numRedundants); }
                             
 						}
 					}