GitLab

First stage commit only. Partial functionality (detailed below), but works and reduces
chance of missing problems.

1. Made exception data structure richer for check_for_stops to allow a number of different
types of exception to to be expressed.

2. Added a new exception type, that of known TGA-stopping Sec-coding transcript.

3. Added data-structure to add_selcys stop checking to allow specification of known
TGA-stopping Sec-coding transcripts.

1. Fix check_for_stops to cope with multiple adjacent internal stops without a loss of codon to AA sync.
Found when running add_selcys.pl on zebrafish for Vega 47.

2. Fix to existing conditional in vega Sec QC script which tests for an anacode bug before deciding to complain
about missing Sec markup for selenoproteins that also stop with TGA, so that this conditional actually spots
this case in more proteins and so cries wolf less often.

fixes when identifying other stops -  1) ribosomal frameshift ignored, 2) stop codon being automatically annotated as a seleno and 3) non numerical values in comments

sub check_for_stops can be given a 3rd parameter, an object with the sub _save_log, to save the logs to. This is optional, ommitting it renders the sub functionally equivalent to the previous version

sub check_for_stops can be given a 3rd parameter, an object with the sub _save_log, to save the logs to. This is optional, ommitting it renders the sub functionally equivalent to the previous version

<ensembl-dev@ebi.ac.uk> to <dev@ensembl.org>.

Formatting of SYNOPSIS code.

Passes unit tests.