Fix issue with wholegenome.interval_list file

[maxulysse]

@klmr

• Fix issue with .interval_list file from the GATK bundle that was not recognized in the CreateIntervalsBed process
• Close wholegenome.interval_list not recognized by CreateIntervalsBed process #56

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[drpatelh]

@maxulysse GATK includes a number of tools for interval manipulation and conversion. Are these not suited to what you are trying to do?
https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_SplitIntervals.php

[maxulysse]

Not really, we designed our intervals file based on the one provided by the broad, but we added some extra infos to group up some intervals.
But I'm willing to have a look into GATK specific intervals tools in some refactoring for a future PR

[drpatelh]

Ok. Looks good to me too in that case 👍