Make genome builds configurable

[ifokkema]

[Intro]

• Design a Genome Build table (id, name, column_suffix, created_by, created_date)
• Create Genome Build table for:
  • For new installs
  • For upgraded installs
• Automatically fill with the standard genome build that has been selected
  • For new installs
  • For upgraded installs
• Allow user to activate a genome build (Add/enable new GB #553).
  • Entry must be created in the Genome Build table.
  • VOG table must be altered (adding start, end, DNA field).
  • Custom DNA column must be created.
  • Transcripts table must be altered (adding start, end fields).
  • Automatically fill in missing positions for transcripts and variants. (Automatically lift over existing variants to all active GBs #600)
• Link to GB VL and GB?add from the Setup.
• Allow user to deactivate a genome build.
  • Only allow the deactivation when all information is mapped on the remaining GBs
  • Entry must be deleted in the Genome Build table.
  • VOG table must be altered (removing start, end, DNA field).
  • Custom DNA column must be deactivated.
  • Transcripts table must be altered (removing start, end fields).
• Show on genome builds VL how "complete" the genome build is
  • If this is too slow, put on the VE or perhaps using AJAX.
• Add field to VOG table to track original submission.
  • Have this registered for existing submissions?
  • Have this registered for new submissions
  • If VOT is the source, this should also somehow track what NC was used for the intronic variants.
• Fix dependencies.
• Add details from multiple genome builds to the API. (Dynamically find and show all active GBs in the LOVD API #589)
• Allow submission starting any genome build.
  • Submission form (Implement VariantValidator for all genome builds in variant data entry form #562)
  • Submission API
• Allow import using any genome build
• Remove refseq_build from TABLE_CONFIG.
  • Fix dependencies.
• Remove data duplication from inc-init.php and inc-sql-chromosomes.php.
  • Fix dependencies.
• There should be a "default" genome build - configurable?
  • Then fix all instances of $this->sSortDefault = 'VariantOnGenome/DNA';