added 2 new columns in the table: canonical_transcript_id and canonical_annotation and the respective methods in the API to get/set this new information

  my ( $current_start, $current_end );
as these variables were being declared twice

(If -outdir is not specified, or if the dir does not exist, then output from bjobs is written to pwd)

script for setting canonical transcript id in the gene table on the basis of simple rules

completely.

file and script for loading analysis descriptions

Added OTTG and change the codes to be 4600, 4610 ad 4620 corresponding to gene, transcript and translation to be consistent with other similar types

Added OTTG and change the codes to be 4600, 4610 ad 4620 corresponding to gene, transcript and translation to be consistent with other similar types

Added OTTG and change the codes to be 4600, 4610 ad 4620 corresponding to gene, transcript and translation to be consistent with other similar types

Swap order of name,coord_system ID in seq_region unique index, and add new index on coord_system ID. Remove redundant name index.

ANALYSE TABLE is run after the index modifications, so this patch may take a few minutes to execute.

Change gene.canonical_transcript to canonical_transcript_id, and add canonical_annotation, DEFAULT NULL

Added hcoverage to pep_check_sql and dna_check_sql. Also added hcoverage to @check_args so that hcoverage is checked when looking at what has already been written.