search

fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
354 stars 47 forks source link

support for gzip stream #73

Closed lindenb closed 5 years ago

lindenb commented 5 years ago

This PR is related to https://github.com/fritzsedlazeck/SURVIVOR/issues/72

it adds a support for g-zipped stream for 'merge'

basically I created a subclass of streambuf that wrap the gzlib (https://www.zlib.net/manual.html) and I use this new class to initialize a istream that reads the vcf

I added a library -lz in the makefile.

I don't have any unit test but it seems to merge with a mix of vcf+vcf.gz files.

I changed some message from 'cout' to 'cerr' and exit with failure (not exit(0) )

fritzsedlazeck commented 5 years ago

Thanks man! Highly appreciated.