Fixed a bug in the count output of seq.error when using multiple processors
working on dereplicate=t issue in chimera.slayer and chimera.perseus, added appendFilesWithoutHeaders to mothurOut. fixed bug in make.contigs with headers. fixed name file overwrite in unique.seqs. fixed seq name mismatch in get.seqs if dups=f. added count file to seq. error command.
Merge remote-tracking branch 'origin'
finished dereplicate changes to chimera commands.  added taxonomy file to subsample command.
make.contigs bug with file option and multiple processors. added make count parameter
removed make count from make.contigs
added end of file character to some type type reads. fixes while testing.
added count file to get.sabund and get.rabund commands. fixed bug in windows paralellization of pairwise.seqs - cutoff was not passed to thread. added otulabels to shared file in remove.rare command.  added check to make sure reorient is only used when paired barcodes are provided.
added name, group and count files to chop.seqs. added intelligent warnings for when you use a group file instead of design file - common bug report.
sffinfo bug with flow grams right index when clipQualRight=0
added method parameter to get.oturep. options method=abundance or distance. default=distance. added summary type to current types saved by mother
added rarepercent and keepties parameters to the filter.shared command.
added get.metacommunity command.
paralellized unifrac.weighted for windows. added get.metacommunity command.  fixed bug in sequence class filterToPos that was effecting pcr.seqs trimming. {For forward primer trimming with aligned sequences and keepdots=t. If the character before the first primer base was a base and not a gap the base was not trimmed.} modified setFilePosFasta in mothurOut class to help with large files on 32bit machines.
added mothurOutJustToScreen function and changed all counter outputs to use it.
added flag to count table read so that commands that don't require the group info can tell countTable to ignore it
paralellized make.table / count.seqs command. added getCopy function to groupMap class.
added adjustDots function to pcr.seqs, keeps sequences aligned in case where primers are found at different locations.
added shared, constaxonomy and label parameter to get.lineage and remove.lineage commands. Allows user to select / remove OTUs that classified to a specific taxonomy or set of taxonomies.
Merge branch 'upstream-master'

Conflicts:
	abstractrandomforest.cpp