Current commit of dev in order to merge BWA branch.
Merge branch 'master' of github.com:Ecogenomics/APP
Merge branch 'bwa'. Additional fixes in previous commit.
APP now reports its current version.
Rarefaction depth is now limited by default (for large samples)
Certain file names have been updated to be more informative.
BWA can now be used as an assignment method (BWA branch merge).

Conflicts:
	app_make_results.pl
Version 2.2.0
Corrected OTU file name error in AppConfig preventing SEQ normalisation.
assign_taxonomy.py can now be multithreaded and use BWA as a taxon assigner during SEQ based normalisation
Samples with hyphens are flagged (these can cause problems due to QIIME sample name handling)
Changed the threads that usearch using during chimera searching (hard-coded - lazy,lazy,lazy...)
Version 2.3.1

Corrected missing module in app_csv2epi.pl.
Changed warning wording in app_make_results.pl.
Version 2.3.2

Increased heap memory of ACACIA to 100G, and also increased verbosity about possible ACACIA failures.
Changed order of output for app_csv2epi.pl in order to make processing on the robot more efficient.
Added new primer to lib/AppPrimers.pm.
Added extra copyright information to app_do_QA.pl.
Version 2.3.3
Added the OTU_TABLES_ONLY flag to the app config file to stop APP after OTU table generation.
App_do_QA.pl will now search for .fa and .fasta in addition to .fna.
Sanity check added after split_libraries.py.
app_do_QA.pl will now halt if no sequences successfully make it past split_libraries.py.
Minor correction to fix Krona.
Version 2.3.4
APP will not crash when during beta diversity when one sample is used.
Fixed user options for custom databases and standardised several parameters.
Trim length default reduced to 250bp.
Version 2.3.5.
Fixed minor error in app_do_QA.pl which caused read counts to be incorrect.
Version 2.3.5.

Corrected version number.
Version 2.3.6
Actually fixed the app_do_QA.pl issue reported to be fixed in 2.3.5
Integrated CDHITOTU into app.
Update app_combine.pl documentation
Massive overhaul of APP.
app_do_QA.pl and app_make_results.pl replaced with app_create_analysis.pl and app_run_analysis.pl.
Code is more modular, modules can be excluded/included from the config file.
CD-HIT-OTU is integrated and is now the default pipeline, in preference to QIIME, for OTU table generation.