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mkirsche / Iris

A module for improving the insertion sequences of structural variant calls
MIT License
29 stars 5 forks source link

no error in absence of bam index #4

Closed wdecoster closed 4 years ago

wdecoster commented 4 years ago

Hi,

Although it's obviously my fault for forgetting to index the bam, I think the messaging about this could be clearer. Iris does not report something is wrong, but rather returns that there are 0 relevant reads for each variant. It took me a while to figure out what was wrong, and I think this should be an error.

Wouter

mkirsche commented 4 years ago

Hi Wouter,

Thanks a lot for the suggestion, and sorry about any extra frustration with debugging it! I'll add a check for that sometime in the next few days and will let you know when it's been updated.

Thank you, Melanie

mkirsche commented 4 years ago

Hi Wouter,

I resolved this issue by having Iris automatically check for the presence of a BAM index and use samtools to create it if it is missing, and this will be added as part of the next conda release. Please let me know if you continue to have this problem!

Best, Melanie

wdecoster commented 4 years ago

Thanks!