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NBISweden / aMeta

Ancient microbiome snakemake workflow
MIT License
19 stars 14 forks source link

switch to abundance quantification in python #69

Closed clami66 closed 2 years ago

clami66 commented 2 years ago

Here, we introduce a simple python script to count occurrences of taxids from one text file in a gzipped sam file. Tests look good, but we can't be absolutely sure that they are correct since the code in the original pipeline contains bugs

Fixes #68

clami66 commented 2 years ago

Tests now pass @percyfal

clami66 commented 2 years ago

I assume the empty foo file got added by mistake? Remove it and then we can merge.

it was obviously integral to the inner workings of the pipeline... but now I have removed it :)