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pritykinlab / guidescanpy

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guidescanpy filter_tag command; minor other tweaks #67

Closed vineetbansal closed 1 year ago

vineetbansal commented 1 year ago

guidescan filter-tag command (with sensible defaults for k0/k1/k2/k3) that sits between guidescan enumerate and guidescan_add_ce.

guidescan_add_ce takes in optional region paramters (for example one invocation might be python rs2/main.py {input.bam_file} {input.fna_file} {output} --contig NC_001133.9 --start 10000 --end 20000 instead of the default), to speed up testing.

I've removed sam_to_bam since I now agree with your original logic of having the rule do what it wants and add an indexing step right after it. That way we can index whatever/whenever we need to for the next step to proceed.

vineetbansal commented 1 year ago

The failed CI job is because the new filter_tag command is not on main yet. Merging this PR will make it pass.