X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerauchimecommand.cpp;h=7ff3989dea527060934b417de22ef5078df7a074;hb=6c2b1e530a5c0bb87040e58a3e410097acdfcc3d;hp=461c3b693c2c79315d1d98263ce55340541496bb;hpb=dc383fb61b6d165a8d36e6108df8bc7129243ae6;p=mothur.git

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 461c3b6..7ff3989 100644
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -1616,7 +1616,7 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
 			string extension = toString(i) + ".temp";
 			
 			uchimeData* tempUchime = new uchimeData(outputFileName+extension, uchimeLocation, templatefile, files[i], "", "", "", accnos+extension, alns+extension, dummy, m, 0, 0,  i);
-			tempUchime->setBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract);
+			tempUchime->setBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract, hasCount);
 			tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract);
 			
 			pDataArray.push_back(tempUchime);
@@ -1748,7 +1748,7 @@ int ChimeraUchimeCommand::createProcessesGroups(string outputFName, string filen
 			string extension = toString(i) + ".temp";
 			
 			uchimeData* tempUchime = new uchimeData(outputFName+extension, uchimeLocation, templatefile, filename+extension, fastaFile, nameFile, groupFile, accnos+extension, alns+extension, groups, m, lines[i].start, lines[i].end,  i);
-			tempUchime->setBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract);
+			tempUchime->setBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract, hasCount);
 			tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract);
 			
 			pDataArray.push_back(tempUchime);
@@ -1761,7 +1761,7 @@ int ChimeraUchimeCommand::createProcessesGroups(string outputFName, string filen
 		
 		
 		//using the main process as a worker saves time and memory
-		num = driverGroups(parser, outputFName, filename, accnos, alns, lines[0].start, lines[0].end, groups);
+		num = driverGroups(outputFName, filename, accnos, alns, lines[0].start, lines[0].end, groups);
 		
 		//Wait until all threads have terminated.
 		WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);