fixed phylo.diversity and made trim.seqs with allfiles=T open one file at a time.

[mothur.git] / pipelinepdscommand.cpp

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index 46081df5466b74ff03e9384cefcbee4ca82997a6..a747aa752389ccb3dd0339c0b33df5d1c8bd37ef 100644 (file)
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -595,7 +595,7 @@ void PipelineCommand::createPatsPipeline(){
                //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 + ")";
+               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
@@ -613,7 +613,7 @@ void PipelineCommand::createPatsPipeline(){
                
                //screen.seqs
                fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "align";
-               thisCommand = "screen.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", name=" + nameFile + "group=" + groupFile + ", optimize=end-minlength)";
+               thisCommand = "screen.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", name=" + nameFile + ", group=" + groupFile + ", optimize=end-minlength)";
                commands.push_back(thisCommand);
                
                //chimera.slayer
@@ -625,7 +625,6 @@ void PipelineCommand::createPatsPipeline(){
                
                //remove.seqs
                string accnosFile = m->getRootName(m->getSimpleName(fastaFile))  + "slayer.accnos";
-               fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "slayer.chimeras";
                thisCommand = "remove.seqs(fasta=" + fastaFile + ", name=" + nameFile + ", group=" + groupFile + ", accnos=" + accnosFile + ", dups=T)";
                commands.push_back(thisCommand);