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.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@490 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@420 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/implicit-config-branch@408 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@342 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@338 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1