idiomatic on experiencing an unexpected system call failure in this
file than die.

and you don't want to die.

pipeline and run them on the LSF.

hive and memory requirement adjusted

added some dependencies between analyses to prevent interferences

        - if more than max_run iterations
        - if all features have been found

run on blocks only if slice is part of the karyotype
run on full slice else

no need to override method transcript_display_xref_sources - diplay xrefs are done in OfficialNaming.pm for zebrafish

Two commits. First is to use a custom factory to let us default to embl, genbank dumps and allow user override [ENSCORESW-226]. Secondly our pipeline was not RC_NAME friendly. We now inherit the default options from hive generic conf and add our own [ENSCORESW-225]

[ENSCORESW-224]. Fix for multi-line SQ lines caused by large sequences being pushed through SeqDumper. Was never an issue before as our slices were never big enough. Applied the same fix to Genbank but it should be less of an issue due to it's formatting meaning we need larger slices to cause the issue.

Added a single warning for running without a CCDS database, and provided an exit for certain no-data situations.

Tests null cases and basic functioning of sorting algorithm.

New utility object for finding canonical transcripts. Refactoring of "set_canonical_transcript.pl" logic.