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vtsyvina / CliqueSNV

MIT License
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Prevent -oe from exceeding the bounds of the haplotype #11

Closed TheWhyofFry closed 3 years ago

TheWhyofFry commented 3 years ago

Hi there

If you provide the -oe option and this value exceed the length of the haplotype, an exception occurs. I'm using CliqueSNV in a pipeline and sometimes it's difficult to detect whether the -os -oe values fall within the bounds of the haplotype. My knowledge of java is minimal and I've implemented a fix (but not in an elegant way) by using an intermediate "end" variable and constraining it to the length. The solution works, but I fear a pull request would be ugly :-)

vtsyvina commented 3 years ago

Hello,

Thanks for letting me know about this bug. I just fixed it with the latest minor version. You can get the latest jar directly from the repo or google drive link.

When running it should show "1.5.6.1" version