amplab / snap

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
https://www.microsoft.com/en-us/research/project/snap/
Apache License 2.0
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Feature request - accept .fa.gz input files #132

Closed haiqu closed 2 years ago

haiqu commented 3 years ago

Seems strange to need extracted .fa files as input when reference genomes are distributed as .fa.gz files, and since the capability is already in the code this should be trivial to implement.

bolosky commented 3 years ago

Yes, we should do this.

From: Rob Judd notifications@github.com Sent: Thursday, December 17, 2020 6:17 AM To: amplab/snap snap@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [amplab/snap] Feature request - accept .fa.gz input files (#132)

Seems strange to need extracted .fa files as input when reference genomes are distributed as .fa.gz files, and since the capability is already in the code this should be trivial to implement.

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bolosky commented 2 years ago

This is done in 2.0.1. As you might imagine, it wasn't as easy as it seemed, or we would have done it earlier.