Support compressed files

bcgsc / NanoSim

Nanopore sequence read simulator

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Support compressed files #117

Closed kmnip closed 3 years ago

kmnip commented 3 years ago

support reading and writing gzip'd files
support reading and writing BAM files
write intermediate SAM output as BAM file with samtools (new dependency)

kmnip commented 3 years ago

@cheny19, @SaberHQ Please review this pull request. Thank you!

SaberHQ commented 3 years ago

Thanks for this @kmnip

I did a high level overview of the scripts and suggested edits and everything looks good for me. I will wait for @cheny19 for some comprehensive reviews as well. Meanwhile, I will try to benchmark it on some datasets and keep you updated on that.

Thanks, Saber.