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paoloshasta / shasta

De novo assembly from Oxford Nanopore reads.
https://paoloshasta.github.io/shasta/
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--Reads.desiredCoverage does to work when RLE is turned off #4

Closed paoloshasta closed 2 years ago

paoloshasta commented 2 years ago

The --Reads.desiredCoverage command line option causes Shasta to crash when the Run-Rength Encoding (RLE) representation of the reads is not used (that is, --Reads.representation is 0). This was first reported by @colindaven in #1.

RLE is turned off in all 4 assembly configurations for ONT R10 reads, so --Reads.desiredCoverage will not work when using one of those configurations.

paoloshasta commented 2 years ago

--Reads.desiredCoverage does work correctly when RLE is in use, which is the case for most Shasta assembly configurations, with the notable exception of the 4 new ones for R10 reads.

paoloshasta commented 2 years ago

Fixed by commit 356c004880718892067ea69ffec64a1ddcc62335. The fix will be in the next release.

paoloshasta commented 2 years ago

This fixed in Shasta 0.11.1.

colindaven commented 2 years ago

Thanks, can confirm this works for me now. If set incorrectly, the error in the log is understandable.