Amptk

* bug fixes for `amptk lulu`, bug fixes for `amptk taxonomy` to better deal with 16S 8 level taxonomy
* added some minor functions to `amptk filter`
* improvement of `amptk illumina3` as well as allowing `--barcode_rev_comp` to reverse complement barcode sequences, i.e. if indexing was done on reverse primer. mapping file is not required now can also pass primers and a barcode faster file for demuxing.
* clean up repo slightly, trying to get conda recipe working.

* bug fix for `amptk filter` and the subtract feature https://github.com/nextgenusfs/amptk/issues/31
* fix menu option https://github.com/nextgenusfs/amptk/issues/33
* added LULU module for OTU curation, see more here: https://www.nature.com/articles/s41467-017-01312-x
* LULU usage: `amptk cluster` --> `amptk filter` --> `amptk lulu` --> `amptk taxonomy` --> `amptk stats`
* added indicator species analysis to `amptk stats`
* several bug fixes for `amptk stats`
* added option to drop specific OTUs prior to running `amptk stats`

* update the ITS database to use newest version of UNITE database version 01.12.2017.

* bug fix for `amptk show` if non gzipped file passed it was removed
* added gzip support for `amptk sample`
* bug fix for `amptk filter` if OTUs and OTU table did not overlap 100% then script would die, added sanity check
* changed `--col_order` in `amptk filter` to be a space separated list (was previously comma separated with no space).

* minor bug fixes for `amptk database`
* update to `amptk filter` to only label potential chimera OTUs if `--calculate all` is passed, i.e. you are using a synthetic mock that won't be in the rest of your samples

* now requires [edlib v1.2.1](https://github.com/Martinsos/edlib) -> thanks to Edlib developer (Martin Šošić) for finding the bug that was preventing full usage of edlib in `amptk`. primer and barcode searches now very fast.
* added a new phyloseq module, `amptk stats` which will run some preliminary community ecology stats on your BIOM output file. requires R and phyloseq
* added support for UNOSIE3 via the `amptk unoise3` command, note you will need to have USEARCHv10 for this script to work.
* updated global alignment taxonomy search to better deal with multiple hits in the reference database
* updated ITS reference database as well as COI database.
* finally wrote some more comprehensive documents, located at http://amptk.readthedocs.io
* several minor bug fixes