X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=pipelinepdscommand.cpp;fp=pipelinepdscommand.cpp;h=0217d392a1e0454be1319b13e9f750d3a1e1d1fc;hb=f09bacac01a842a74c1c1b69070852cc969ff506;hp=a747aa752389ccb3dd0339c0b33df5d1c8bd37ef;hpb=83c530c577250f2bc4c3443b33d97449abf40f36;p=mothur.git

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index a747aa7..0217d39 100644
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -590,13 +590,13 @@ void PipelineCommand::createPatsPipeline(){
 		
 		//sff.info command
 		string thisCommand = "sffinfo(sff=" + sffFile + ")";
-		commands.push_back(thisCommand);
+		//commands.push_back(thisCommand);
 		
 		//trim.seqs command
 		string fastaFile = m->getRootName(m->getSimpleName(sffFile)) + "fasta";
 		string qualFile = m->getRootName(m->getSimpleName(sffFile)) + "qual";
-		thisCommand = "trim.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", allfiles=T, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, oligos=" + oligosFile + ", qfile=" + qualFile + ")";
-		commands.push_back(thisCommand);
+		//thisCommand = "trim.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", allfiles=T, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, oligos=" + oligosFile + ", qfile=" + qualFile + ")";
+		//commands.push_back(thisCommand);
 		
 		//unique.seqs
 		string groupFile = m->getRootName(m->getSimpleName(fastaFile)) + "groups";