GitLab

distribution.

database in GFF format (STDOUT).

Added code to delete names/GO terms if the -delete_only option is specified. Added code to check whether
-registryconf is submitted as a string from the submit_projections.pl script or as a file on the command
line.

a) added unused_priority to the order list as this now contains the number of times that trancript name was used and is need to make sure that the gene name is the same as the transcripts. b) make sure there is a description else we get a ton of warning regarding undefined vars

For offical naming take the gene name of the most comman transcript name. Also remove any version numbers from the transcripts

commented out the finding the best gene match as we only need the best transcript match. Having both confuses Biomart anyway

needed but can be useful so keeping a record of it.

* If there is only one protein_coding transcript in a gene, use it as
  the canonical transcript but make sure it doesn't have internal stops.

* If a seq_region_name is given, zero set the canonical_transcript_id
  and canonical_annotation, otherwise zero set all
  canonical_transcript_ids.

Added minimal doc.

processed_transcript', if gene biotype is protein_coding.

command line arguments standardized to the ones used in the genebuild scripts ( dbhost dbname dbport ... )

the stable ID mapping scripts.  Fixes breakage for human.

Do not repair automatically.
Add informationl blurb at end of execution.