X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pipelinepdscommand.cpp;h=a747aa752389ccb3dd0339c0b33df5d1c8bd37ef;hb=83c530c577250f2bc4c3443b33d97449abf40f36;hp=26969d81c7b6d95a0f7c603489be1da984ea7d99;hpb=257eaa172451ede9d63a0715f6cdb7336a52996b;p=mothur.git

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index 26969d8..a747aa7 100644
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -590,38 +590,38 @@ 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=F, 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";
 		qualFile =  m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
 		fastaFile =  m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";
-		//thisCommand = "unique.seqs(fasta=" + fastaFile + ")"; 
-		//commands.push_back(thisCommand);
+		thisCommand = "unique.seqs(fasta=" + fastaFile + ")"; 
+		commands.push_back(thisCommand);
 		
 		//align.seqs
 		string nameFile = m->getRootName(m->getSimpleName(fastaFile)) + "names";
 		fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "unique" + m->getExtension(fastaFile);
-		//thisCommand = "align.seqs(processors=" + toString(processors) + ", candidate=" + fastaFile + ", template=" + alignFile + ")";
-		//commands.push_back(thisCommand);
+		thisCommand = "align.seqs(processors=" + toString(processors) + ", candidate=" + fastaFile + ", template=" + alignFile + ")";
+		commands.push_back(thisCommand);
 		
 		//screen.seqs
 		fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "align";
-		//thisCommand = "screen.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", name=" + nameFile + ", group=" + groupFile + ", optimize=end-minlength)";
-	//	commands.push_back(thisCommand);
+		thisCommand = "screen.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", name=" + nameFile + ", group=" + groupFile + ", optimize=end-minlength)";
+		commands.push_back(thisCommand);
 		
 		//chimera.slayer
 		fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "good" + m->getExtension(fastaFile);
 		nameFile = m->getRootName(m->getSimpleName(nameFile)) + "good" + m->getExtension(nameFile);
 		groupFile = m->getRootName(m->getSimpleName(groupFile)) + "good" + m->getExtension(groupFile);
-		//thisCommand = "chimera.slayer(processors=" + toString(processors) + ", fasta=" + fastaFile + ", template=" + chimeraFile + ")";
-	//	commands.push_back(thisCommand);
+		thisCommand = "chimera.slayer(processors=" + toString(processors) + ", fasta=" + fastaFile + ", template=" + chimeraFile + ")";
+		commands.push_back(thisCommand);
 		
 		//remove.seqs
 		string accnosFile = m->getRootName(m->getSimpleName(fastaFile))  + "slayer.accnos";