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mossmatters / HybPiper

Recovering genes from targeted sequence capture data
GNU General Public License v3.0
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`hybpiper stats` and `hybpiper retrieve_sequences` take a very long time when processing compressed sample folders (HybPiper version 2.3.0) #161

Open chrisjackson-pellicle opened 2 hours ago

chrisjackson-pellicle commented 2 hours ago

Stats and sequence recovery commands take a very long time when processing compressed (*.tar.gz) sample files with HybPiper version 2.3.0

chrisjackson-pellicle commented 2 hours ago

Known issue - each compressed sample file should only be uncompressed once, and sample files should be processed in parallel using multiprocessing. Currently working on a fix for HybPiper version 2.3.1