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louiejtaylor / grabseqs

A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA
MIT License
105 stars 16 forks source link

For SRA downloading, make sure pigz zips only the correct sequence files #12

Closed louiejtaylor closed 5 years ago

louiejtaylor commented 5 years ago

This is extremely unlikely to be an issue in practice, but if for some reason an individual were to be downloading two accession numbers such that one accession number was a substring of another accession number, pigz might clobber the shorter accession number because of the way you compress files.

louiejtaylor commented 5 years ago

Note: double check the utils.check_existing function but I think this fixed!

You should use that func on line 112 of sra.py though...

Edit: it does not. However, using the utils.build_paths function should!