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Buggy BioPerl warning too verbose #168

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iimog opened this issue May 7, 2021 · 2 comments
Open

Buggy BioPerl warning too verbose #168

iimog opened this issue May 7, 2021 · 2 comments
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@greatfireball
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@iimog
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iimog commented May 7, 2021

The check for the Bioperl revcom issue is very useful but the logging is far too verbose. When I run AliTV I get one of these messages (depending on the machine):

INFO - MAF input file detected, but Bioperl is bugfree... Therefore, workaround for revcom issue is not activated

or

INFO - MAF input file and buggy BioPerl detected... Therefore, workaround for revcom issue activated

repeated many many times, poluting the output. This message printed once (and not once per maf import) would be sufficient as the BioPerl version does not change during a run.
@iimog
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iimog commented May 7, 2021

It also tends to confuse users e.g. AliTVTeam/AliTV#163

@greatfireball
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I totally agree! Will have a look on the issue on the weekend.

@greatfireball greatfireball self-assigned this May 7, 2021
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