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bcgsc / ntEdit

✏️ Genome assembly polishing & SNV detection
GNU General Public License v3.0
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counting Bloom filter with ntEdit #42

Closed jwcodee closed 11 months ago

jwcodee commented 11 months ago

on line #81: -p, minimum k-mer presence threshold..

By "presence" do you mean "coverage" (or "multiplicity")?

Yes. I have amended the wording

warrenlr commented 11 months ago

I like all your suggestions @lcoombe, thank you for your review.

I agree with a more succinct parameter definition (and organization of CBF-specific params in the menu), let's go with: -p minimum k-mer coverage threshold (CBF only) -q maximum k-mer coverage threshold (CBF only)

The readme will document additional & specific info on the new parameters

to clarify on another of @lcoombe points, let's please also edit those:

-r, Bloom filter (BF) or counting BF (CBF) file (generated from ntHits v1.0.1+), REQUIRED -e, secondary BF with k-mers to reject (generated from ntHits v1.0.1+), OPTIONAL - NOT NEEDED with CBF

warrenlr commented 11 months ago

also, when the time comes, @parham-k and @jwcodee, would you be able to make edits to ntedit-make to reflect the new options offered in both nthits1 and ntedit2? We should also add ntcard to it, since it was previously coupled with nthits 0.0.1. This will help guide the users on how to properly set things up / run in a pipeline.

jwcodee commented 11 months ago

@parham-k I've made some updates to the README, Do you think you can edit the rest? Also, do you know what's going on with the mac CI? Never seen that error before