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mkirsche / Jasmine

Jasmine: SV Merging Across Samples
MIT License
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Correctly parseInt the SUPP entry, not the string itself. #46

Open ASLeonard opened 1 year ago

ASLeonard commented 1 year ago

Hi, I'm not sure what triggers this if/else condition as I've used Jasmine for many other VCFs without issue, but this line will trivally cause a crash as "SUPP" is not an integer.   https://github.com/mkirsche/Jasmine/blob/12b3862345b21ae5bb659ca077cfdfb021fef3d4/src/VariantOutput.java#L407   Other lines in the file have 

Integer.parseInt(entry.getInfo("SUPP"));

  and replacing the issue on L407 with that fixes this problem.

I'll still test this on some old datasets to make sure there are no unintended consequences, but should be harmless.   Best, Alex

YannLeGuen commented 8 months ago

This would probably solve the following issue https://github.com/mkirsche/Jasmine/issues/58