search

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

Separate main function. #8

Closed joshuak94 closed 5 years ago

joshuak94 commented 5 years ago

This pull request does a few things.

  1. Create a sviper.h file in include.
  2. Move parsing the command line, reading and writing of VCF, prepping file handles for parallel processing, and polishing of variants all into separate functions in sviper.h.
  3. Creates a struct Auxiliary for storing and moving file handles and command options between functions.
joshuak94 commented 5 years ago

I moved the auxiliary and io stuff into their own files, and removed using namespace seqan from sviper.cpp and sviper.h

joshuak94 commented 5 years ago

@smehringer Done!

joshuak94 commented 5 years ago

@smehringer wait don't merge yet!

joshuak94 commented 5 years ago

Okay, now you can merge.

smehringer commented 5 years ago

This was close

smehringer commented 5 years ago

We need to add some unit tests