change to .gitignore
Merge remote-tracking branch 'mothur/master'
dunno
Merge remote-tracking branch 'mothur/master'
fixed subsample name file name issue.  added count parameter to cluster command. added read to readColumn and readMatrix that uses a count table. added functions to countTable class to work with clusters reads.
Merge remote-tracking branch 'mothur/master'
added count file to cluster.classic and cluster.split. modified splitting classes to use the count file.
paralellized chop.seqs
changes while testing 1.27
added SequenceCountParser class to parse the count table by group. added count parameter to chimera.perseus.
added count parameter to chimera.slayer command
Issue #25: [c++] [integration] added classify.shared command reference to commandfactory.cpp file
added count file to chimera.uchime. found issue with uchime program that indicated order mattered.  added sort to mothur.h and reported to edgar.
added code to format fast files for uchime.  started work on sff.multiple command
Issue #25: [c++] [integration] finishing up the integration
Issue #25: [c++] [integration] splitcriteria and otupersplit parameters handled
added oligos, pdiffs, bdiffs, ldiffs, sdiffs, tiffs parameters to sffinfo to allow for spitting the sff file by barcode. working on sff.multiple command.
Issue #25: [c++] [integration] handling of inputDir and outputDir (partially)
Issue #25: [c++] [integration] enabling code for SharedRAbundVector
Issue #25: [c++] [integration] re-indenting some of the codes for better readability