Working on seq.error changes
Merge remote-tracking branch 'mothur/master'
Merge remote-tracking branch 'mothur/master'
Changes to seq.error so that an alignment is not necessary
test
test
test
Merge remote-tracking branch 'mothur/master'
TEST
fix bug in unaligned seq.error / chimeraref
added filter.shared command. fixed lci and uci for thetayc calc
Merge remote-tracking branch 'origin/master'
added dereplicate parameter to chimera.slayer and chimera.persues. added minnumsamples and minpercentsamples to filter.shared.  fixed output names in cluster commands. added count parameter to parse.list. improved speed and memory requirements on sens.spec. added debugging code to some phylotree functions.
fixed bug in pre.cluster with output file name change and other bugs while testing 1.29.0
added topdown parameter to pre.cluster.  added more debugging output to bayesian class. fixed mpi compile issue in cluster.split.  fixed 32bit constant declarations in refchimeratest.cpp. fixed some commandName issues for gui interface
fixed seq. error align=f issue. added std and ave calcs to mothurout. working on unifrac bug report
added primer.design command.  fixed bug with linux unifrac subsampling, metastats output filename, venn command is no shared outs,  added check for ':' in sequence names to avoid trouble with trees. added format parameter to make.contigs.
added checks to make sure windows processes completed their tasks.
added get.dists and remove.dists commands. fixed bug in trim.seqs windows paralellization that caused blank groups in group file. added list and shared file to get.otulabels and remove.otulabels. added list file to list.otulabels.
added *.count.summary file to count.groups command. added deltaq and insert parameters to make.contigs and changed contigs.report file. added illumina1.8+ format to fast commands. added contigsreport, align report and summary files to screen.seqs to allow files to be screened using their inputs.  added minoverlap, ostart, oend, mismatches, maxn, minscore,maxinsert, minsim parameters to screen.seqs. added optimization types of minoverlap, ostart, oend, mismatches, maxn, minscore,maxinsert, minsim to screen.seqs.  added getNumNs function to sequence class. working on Windows \\ issue.