added sff.multiple command. fixed issue with windows paralellization in chimera...

[mothur.git] / chimerauchimecommand.cpp

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 461c3b693c2c79315d1d98263ce55340541496bb..7ff3989dea527060934b417de22ef5078df7a074 100644 (file)
--- 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);