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Merged
merged 2 commits into from
Feb 10, 2023
Merged

Force full-length ivar consensus builds #5115

merged 2 commits into from
Feb 10, 2023

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@wm75
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@wm75 wm75 commented Feb 3, 2023

FOR CONTRIBUTOR:

  • - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • - License permits unrestricted use (educational + commercial)
  • - This PR adds a new tool or tool collection
  • - This PR updates an existing tool or tool collection
  • - This PR does something else (explain below)

@wm75
Force full-length ivar consensus builds
88c9ddc 
This requires the -a option of samtools mpileup or zero-coverage regions
at the ref sequence ends will silently be dropped and a truncated
consensus be produced.
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wm75 commented Feb 3, 2023

@pvanheus not quite sure how this one could go unnoticed until now.

@wm75 wm75 added the virology Issues related to better support for virology of SARS-CoV-2, MPXV and more. label Feb 3, 2023
@bernt-matthias
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bernt-matthias commented Feb 5, 2023

Please also check in the help section and report upstream https://github.com/andersen-lab/ivar/blob/d0e2ad0e6be69307771a5d36c573ffba578f4ce0/pipeline_consensus/Snakefile#L34

@wm75
More fixes to the consensus tool
40d1f00 
- Protect params against integer overflow
- Make "-n -" option work and simplify choice of min depth threshold action
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wm75 commented Feb 6, 2023

@bernt-matthias oh no, don't make me look into too much detail - only unearthing more bugs 🤯

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wm75 commented Feb 6, 2023

and report upstream

done in andersen-lab/ivar#144

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wm75 commented Feb 6, 2023

integer overflow issue reported, too: andersen-lab/ivar#145

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bernt-matthias commented Feb 7, 2023

Then lets merge?

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wm75 commented Feb 10, 2023

Yes, I think so. Thanks for the review @bernt-matthias !

@wm75 wm75 merged commit fc9887d into galaxyproject:main Feb 10, 2023
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@wm75 @bernt-matthias @bgruening