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Reduce times input file is opened #37

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merged 13 commits into from
Dec 3, 2015

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andrewjpage
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Reduce the number of times the input file is opened from 6 to 2. Partially addresses #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. #33

Deleted unused files.

@bewt85 bewt85 self-assigned this Dec 3, 2015
andrewjpage added a commit that referenced this pull request Dec 3, 2015
Reduce times input file is opened
@andrewjpage andrewjpage merged commit d62351a into sanger-pathogens:master Dec 3, 2015
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2 participants