//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";