Merge branch 'release/v1.1'
Merge branch 'release/1.2'
Merge branch 'release/1.2'
Merge branch 'release/1.2.6'
Merge branch 'release/1.3.0'
fixes missing readme in pypi pkg
fixes merge conflicts
Merge branch 'release/1.4.1'
Merge branch 'release/v1.4.2'
Merge branch 'release/1.4.3'
Merge branch 'develop'

* develop: (67 commits)
  Made changes to statistics, so that stats are calculated for both pathogens only and pathogens + (pathogens and human)
  Removed stuff that's not right
  Added script to remove duplicated genes
  Make the tests use a temporary location
  Make the tests actually work this time
  Test fixes
  Added index documentation
  Fixed the authentication. Authenticate against the specified DB, not the admin DB, if we have a username and password
  Added a doc file to track the changes for the indexing planned to help with sharding. No definitive changes yet, but worth documenting in progress.
  Changed the index to improve subtraction performance
  Added various extensions to .gitignore handy for testing
  Modified the gra.sh to use a local library for running Perl and readscan.pl, removing the non-core dependencies. This makes the pipeline easier to deploy in protected environments.
  modified subtraction so it can calculate gra with lookup files provided
  fixed the bug in filter_stats to do with bg filtering
  added the creation of the bg project from get go
  added the creation of the bg project from get go
  added filtering with a bg model
  added parameters when runnning stats with a bg model
  Fixed the search pattern matching for phages
  Refactored the statistics handling to use more common calculations where possible. Also included initial tagging code.
  ...

Conflicts:
	README
Update setup.py

Change version number
added data dir
updated capsid's version
new version of the pipeline
merge
Merge branch 'develop'
updated version
fixed version