The paper (from `Mutalyzer 2.0/`) is now in the `mutalyzer-manuscript`
repository, while all presentations, posters and abstracts are now in
the `mutalyzer-presentations` repository.

Genome assembly definitions for GRCh36, GRCh37, and GRCm38 are included
as JSON files in `extras/assemblies`.

This is The Good Stuff. The entire test suite can now be run without
having to setup a database, running the batch checker, any of the web
services or the website. It even passes without an internet connection.
In, like, 30 seconds! Awesome!

This means tests don't randomly fail after some reference sequence
changes on the NCBI server and it doesn't take an entire configured
server with mapping database setup to run the tests. Those are things
of the past! No more frustrations, Mutalyzer is testable!

Going down now...

The mountain screamed three times today
I guess it thought it'd like to play
How much does one have to pay
To fry a peak and melt away
Launching titan's breath on mine
The sweating measure lands on time

And the old man, down by the river
Well he walks up and he walks on down
To the spaceship that's parked at your doorstep
And it's waiting to take you away now

Goin' down now
Goin' down now

Looking for the rate that crowed
He's hooked up down in Mexico
Slap my nerve now give me more
It's my disaster friend, not yours

And the old man, down by the river
Well he walks up and he walks on down
To the spaceship that's parked at your doorstep
And it's waiting to take you away now

And the last one, it's down by the river
Where he gets up and he walks on down
To the spaceship that's parked at your doorstep
And it's waiting to take you away now

It's down by the river, it's always this way now
It's down by the river, it's always this way now

Going down now
Going down now
now, now, now

down, down, down

This includes changing a lot of routes and parameter names to be more
consistent. We try to remain backwards compatible as much as possible
by providing redirects from old routes and parameter names.

Now that we ported the database to SQLAlchemy, we remove the obsolete Db
module and all references to it.

The Redis client automatically falls back to a mock Redis server if no
Redis server is configured. Therefore, a Redis server is not needed to
run Mutalyzer. You'll just not get any aggregate stat counts over
different runs.

This introduces a proper notion of genome assemblies. Transcript
mappings for alle genome assemblies are in the same database, which
is better for maintenance. Updating transcript mappings is also
simplified a lot, especially from NCBI mapview files where we now
require a preprocessing sort on the input file.

Overall, this port touches a lot of Mutalyzer code, so beware.

See Trac ticket #148

This involves making the SQLAlchemy session reconfigurable at run-time,
which is done automatically on updating the Mutalyzer configuration using
configuration update callbacks.

Port the entire batch job infrastructure, including scheduler, to use
the SQLAlchemy ORM instead of the old Db module.

Warnings were logged with message level 3, which is for errors, and
therefore interpreted as errors (ignoring the batch entry result).

Remove the dependency on configobj and have default values for all
configuration settings. User settings are defined in a Python module
pointed to by the MUTALYZER_SETTINGS environment variable.

We also clean up many configuration settings and remove some that
are no longer used.

We no longer look for /etc/mutalyzer/config and ~/.config/mutalyzer/config
since it is too low level and inflexible. The user should now specify the
location of the configuration file in the MUTALYZER_SETTINGS environment
variable (or the file mutalyzer.conf in the current directory is tried).