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mdshw5 / pyfaidx

Efficient pythonic random access to fasta subsequences
https://pypi.python.org/pypi/pyfaidx
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fool proof faidx .bed file documentation #177

Closed darked89 closed 3 years ago

darked89 commented 3 years ago

Hello,

Since probably I was neither the first nor the last bitten by the 1-based faidx command line coordinates and a say region.bed 0-based ones it may make sense to add:

-b BED, --bed BED     bed file of regions (zero based)

Hope it helps,

DK

mdshw5 commented 3 years ago

Thanks for the suggestion. Indeed 0-based vs 1-based start coordinates will be confusing Bioinformaticians for decades to come. I’ll post the coordinate description here for posterity and release a new version with this change.