fixed bug with aligner and longest base. added deunique.seqs command.

[mothur.git] / pipelinepdscommand.cpp

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index a747aa752389ccb3dd0339c0b33df5d1c8bd37ef..0217d392a1e0454be1319b13e9f750d3a1e1d1fc 100644 (file)
--- 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";