cerebra

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Bumps [numpy](https://github.com/numpy/numpy) from 1.18.1 to 1.22.0. Release notes Sourced from numpy's releases. v1.22.0 NumPy 1.22.0 Release Notes NumPy 1.22.0 is a big release featuring the work of 153 contributors spread...

dependabot[bot]

count-variants not runnable without specifying cosmicdb

1

`count-variants` module cannot be run without specifying a path to a cosmic database file this is a relatively easy fix

lincoln-harris

linking https://github.com/bioconda/bioconda-recipes/pull/23260 tried to add recipe to bioconda. for now failing due to `hgvs` dependency....there is no bioconda or conda-forge recipe for `hgvs` until this exists we wont be able...

lincoln-harris

pysam build fails on python3.8

5

this is a known issue: https://github.com/jbloomlab/alignparse/issues/58 one way to get around it is perhaps a conda installation of `pysam`?

lincoln-harris

make germline-filter module more robust

2

right now it only works if you have a metadata file with a very specific format > cell_id,patient_id sample1,gl_sample1 sample2,gl_sample1 sample3,gl_sample2 sample4,gl_sample2 sample5,gl_sample2 would be nice if we could loosen...

lincoln-harris

add prebuilt index for genome.fa

2

can we add a prebuilt index for the human genome .gtf / .fa that would load much faster? hg38.fa -> 3 Gb hg38.gtf -> 144 Mb

lincoln-harris

in `mutations_table.py`, if a vcf record reports a hit to an intronic region (we think), it will NOT be included in the final table - this is because while the...

lincoln-harris

look into potential changes in mutation_counts functionality due to GenomePosition.from_vcf_record change

1

rvanheusden

I've found that BEDtools seems to convert 1-based genome position strings into 0-based ones. Perhaps GenomePosition.from_str should offer an argument allowing one to indicate if the string is 0-based or...

rvanheusden

Bumps [setuptools](https://github.com/pypa/setuptools) from 47.3.1 to 65.5.1. Release notes Sourced from setuptools's releases. v65.5.1 No release notes provided. v65.5.0 No release notes provided. v65.4.1 No release notes provided. v65.4.0 No release...

dependabot[bot]