Reduce the number of times the input file is opened from 6 to 2. Partially addresses https://github.com/sanger-pathogens/snp_sites/issues/26 but we have to do 2 passes on the file so that we dont end up reading it all into RAM.
This also manually merges with Bens last update (2.0.3).
Added a switch to compile on Linux with -lrt and everything else without.
Removed subunit because its not needed on all systems - it gets added in a patch when being built on Debian. https://github.com/sanger-pathogens/snp_sites/issues/33
Reduce the number of times the input file is opened from 6 to 2. Partially addresses https://github.com/sanger-pathogens/snp_sites/issues/26 but we have to do 2 passes on the file so that we dont end up reading it all into RAM.
This also manually merges with Bens last update (2.0.3).
Added a switch to compile on Linux with -lrt and everything else without. Removed subunit because its not needed on all systems - it gets added in a patch when being built on Debian. https://github.com/sanger-pathogens/snp_sites/issues/33
Deleted unused files.