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smehringer / SViper

Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact (Illumina) reads.
BSD 3-Clause "New" or "Revised" License
32 stars 8 forks source link

Add threads and output prefix to option constructor. #13

Closed joshuak94 closed 4 years ago

joshuak94 commented 4 years ago

Currently, other tools using SViper as a library cannot easily change the threads. This allows threads to be set on construction along with specifying the output prefix.

smehringer commented 4 years ago

there is a conflict

joshuak94 commented 4 years ago

@smehringer Fixed!

joshuak94 commented 4 years ago

@smehringer I will do that, but just wanted to point out that this line is then redundant: https://github.com/smehringer/SViper/blob/72d1e0c3932543adef79765d29c37ff9fca31a8a/include/sviper/sviper.h#L101

Because the user will either call SViper from the command line, meaning the argument parser will set threads to std::thread::hardware_concurrency() by default in the line above, or the user will use SViper as a library, where they then have to construct the CmdOptions struct with the given constructor.