Until now, the name checker form used POST requests. As a special case for
linking from LOVD, GET requests were handled by showing results without the
full interface (header, menu, etc). Ordinary linking was done to a separate
checkForward location which then set a cookie with the variant name and a
redirect to the name checker results. This was all very hackish and somewhat
broken (see Track issue #94).

This commit refactors the name checker to use GET requests, so ordinary
bookmarking of result pages is possible. All old entrypoints are handled with
a redirect for backwards compatibility.

Worth mentioning is that variant descriptions in the name checker are now
limited in length by the maximum query string length. However, this maximum
is several thousand characters with Internet Explorer having the lowest
maximum of just over 2000. Longer descriptions are not practically checked
with the name checker web interface anyway, so this should not be a problem.


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For UD slices we also generate g. descriptions on the chromosome reference. We
now also apply the roll rule there and use correct ranges and sequences on the
reverse strand. Fixes #75.


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During import of the NCBI transcript mappings, CDS start or stop positions
were not picked up for some transcripts (where these are on exon boundaries).

Bug reported by S Venkata Suresh Kumar.


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For use by LOVD (NGS variants import, Jerry Hoogenboom), implement the SOAP
webservice method getTranscriptsMapping. The calling signature is the same as
for the existing getTranscriptsRange method, but the new method returns more
than just the transcript names.


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Previously, the 'color' field in the BED track we provide for the Genome
Browser was set to the empty string, but Gerard informed us that this is not
(always) handled correctly:

   Expecting number field 5 line 2 of https://mutalyzer.nl/bed?..., got +

We now explicitely set the 'color' field to '0'.


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Fixes #74.


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The old way of using the configuration file was by instantiating a Config
object which read the file. This instance was passed to every function and
object that might need it.

The new way is by simply calling config.get('name') to get the configuration
value for 'name'. This lazily reads the configuration file and the contents
are cached for future calls.


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Add optional gene argument to the numberConvertion webservice method. If
present, it will convert genomic variants to any transcript of the given
gene, no matter how far away they are located (but on the same chromosome
of course). Fixes #70.



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Until protein reference sequences are supported, give an error with a message
instead of crashing. Fixes #62.


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The fix is a hack, basically copying the same functionality from the
namechecker. I think this should eventually be merged somehow.

Fixes #63


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- Issue a warning instead of an UD number when a user uploads something
  that is not a genbank file (fixes #59).
- Fix a Heisenbug in the batch job unit tests. Wait a little before
  downloading the batch job results.


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Convert the 'hg18.map' and 'hg19.map' tables are to 'hg18.Mapping' and
'hg19.Mapping'. These tables are now updated with mapping info from the
NCBI instead of the UCSC.

Also added database and configuration file migration scripts.

extras/config.example:
- Remove configuration values for UCSC updates.

extras/post-install.sh:
mutalyzer/Mapper.py:
mutalyzer/Db.py:
- Use 'Mapping' table instead of 'map' table.

extras/cron.d/mutalyzer-mapping-update:
mutalyzer/Mapper.py:
mutalyzer/Db.py:
- Get mapping updates from the NCBI.

extras/migrations:
extras/post-upgrade.sh:
- Automated migration scripts.



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