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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
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SURVIVOR stats with compressed file #98

Open wdecoster opened 5 years ago

wdecoster commented 5 years ago

Hi Fritz,

I'm not sure bgzipped compressed files (or compressed files at all) are supported, but at least no error is raised. When I run SURVIVOR stats test.vcf.gz 30 -1 -1 test-stats I get:

Processing: 705
Parsing done: 
Tot DEL DUP INS INV TRA
657 584 0   73  0   0

However, when running the uncompressed file SURVIVOR stats test.vcf 30 -1 -1 test-stats I get:

Processing: 71983
Parsing done: 
Tot DEL DUP INS INV TRA
71983   45971   806 17361   4287    3558

So something is at least fishy here. If compressed files are not supported then I guess an explicit error would be appropriate :)

Cheers, Wouter

fritzsedlazeck commented 5 years ago

Hey Wouter, good point. I am never checking if a file is not a standard VCF vs. gz or something else.... Cheers Fritz