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KolmogorovLab / Severus

A tool for somatic structural variant calling using long reads
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Allow VNTR BED to be compressed #16

Open awgymer opened 3 months ago

awgymer commented 3 months ago

It would be quite useful if the program was able to handle the --vntr-bed being supplied as a .gz file compressed with bgzip as this allows the same file to be used as elsewhere which require an indexed bed file, which can be quite common in bioinformatics tools and workflows.

It may be as simple as replacing the current open with fileinput.hook_compressed docs.

aysegokce commented 3 months ago

Hello @awgymer, Thank you for the suggestion. We will incorporate it in the next releases. Ayse