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Test cases now pass, we have a capture warns asserting for known bad scenarios and use the Test::Builder code to see if we want to do to screen warning for test cases. Not sure how un # lines in TAP are dealt with; we may want to substitute STDOUT/STDERR for something which can delegate to Test::Builder for note()

Trying to improve the current test cases. Accidentally caused some issues from rerunning the code multiple times as well

[ENSCORESW-238]. Highlighted by Ken Youens-Clark on dev. We call show_valid_species() without a reference to $self

Script used to decode what canonical assignment says has occured during a run. The script accounts for most issues apart from those nasty ones in which case you must firgure that out yourself.

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