Merge branch 'master' into dev-ml
re-enabling the destructor to enable deletion of dynamically allocated memory.
added debugging to otu.association
Merge remote-tracking branch 'origin'
citation changes for 1.31.0
case sensitive include statement caused issues for Unix systems.
added rename.seqs command.
get.seqs not renaming sequences correctly for dups=f. unique.seqs crash when count table had group data.
added make.lefse command.  fixed bug in make.contigs with trimming reverse barcodes and primers. removed extra names check from classfier.  changed minlength default in trim.seqs to 1. added readConsTax function to mothurOut
mgcluster with count file needed to create a nameMap to pass to readBlast like the name file does
test change
added kruskal.wallis command. added worked on make.lefse. working of lefse command. fixed bug in trim.oligos when there was an exact match to paired primers or barcodes that overlapped causing the sequence to be shorter than the barcodes and primers.  added design map class. added kruskal wallis and wilcoxon functions to linear algebra class.
Merge remote-tracking branch 'origin'
fixed problem where order=B was not checking for the maximum homopolymer length
Merge remote-tracking branch 'mothur/master'
asdf
Merge remote-tracking branch 'upstream/master' into dev
files for eclipse CDT
function for calculating confusion matrix added
Merge pull request #43 from rafi-kamal/dev

Confusion Matrix Implementation