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itmat / rum

RNA-Seq Unified Mapper
http://cbil.upenn.edu/RUM
MIT License
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Don't use SAM file produced by the junction script #173

Closed mdelaurentis closed 11 years ago

mdelaurentis commented 11 years ago

Greg found a bug in the way the junction script modifies the SAM file:

The latest version outputs a modified sam file, but there's a subtle case where it modifies one read but doesn't modify the paired end and they then become inconsistent. I looked at the code and there's no easy fix. So for now, I think we should just not output that modified sam file and have the pipeline just proceed with the original.