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Convert 'map' table to 'Mapping' and use NCBI for updates.
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
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- INSTALL 11 additions, 9 deletionsINSTALL
- README 8 additions, 3 deletionsREADME
- bin/mutalyzer 6 additions, 2 deletionsbin/mutalyzer
- bin/mutalyzer-cache-sync 5 additions, 3 deletionsbin/mutalyzer-cache-sync
- bin/mutalyzer-mapping-update 59 additions, 0 deletionsbin/mutalyzer-mapping-update
- bin/mutalyzer-ucsc-update 0 additions, 54 deletionsbin/mutalyzer-ucsc-update
- extras/config.example 0 additions, 6 deletionsextras/config.example
- extras/cron.d/mutalyzer-mapping-update 3 additions, 0 deletionsextras/cron.d/mutalyzer-mapping-update
- extras/cron.d/mutalyzer-ucsc-update 0 additions, 2 deletionsextras/cron.d/mutalyzer-ucsc-update
- extras/migrations/001-db-gbinfo-add-created.migration 69 additions, 0 deletionsextras/migrations/001-db-gbinfo-add-created.migration
- extras/migrations/002-db-map-to-mapping.migration 160 additions, 0 deletionsextras/migrations/002-db-map-to-mapping.migration
- extras/migrations/003-config-remove-ucsc.migration 25 additions, 0 deletionsextras/migrations/003-config-remove-ucsc.migration
- extras/migrations/004-cron-ucsc-to-ncbi.migration 24 additions, 0 deletionsextras/migrations/004-cron-ucsc-to-ncbi.migration
- extras/migrations/README 18 additions, 0 deletionsextras/migrations/README
- extras/post-install.sh 45 additions, 122 deletionsextras/post-install.sh
- extras/post-upgrade.sh 6 additions, 0 deletionsextras/post-upgrade.sh
- mutalyzer/Db.py 202 additions, 372 deletionsmutalyzer/Db.py
- mutalyzer/Scheduler.py 2 additions, 2 deletionsmutalyzer/Scheduler.py
- mutalyzer/config.py 0 additions, 3 deletionsmutalyzer/config.py
- mutalyzer/mapping.py 334 additions, 106 deletionsmutalyzer/mapping.py
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