broadinstitute/viral-ngs — pull request #31 by iljungr (2014-11-05 04:19:31+00:00)
Title: Irwin mvicuna

- Implemented dup_remove_mvicuna, including tool installation and unit test.
- Minor improvement to TestBmtagger (call parser_... and main_... instead of low level utility).

Issues:
- For linux I just copied the mvicuna tool from broad. For mac, I was able to build it from source (from broad) after installing gcc-4.9 and adjusting the make file. I put these two binaries in scripts/mvicuna/linux64/mvicuna and scripts/mvicuna/MacOSX/mvicuna. That's a funny place to put binaries. We should probably either put them somewhere else in a new directory (binaries?), or rename "scripts" to something else (broadUtils?).
- I don't really know how to make a good test because I don't have much idea of what mvicuna is supposed to do, since there's no documentation except the output with -h. I made an input file with some duplication, and it does some kind of duplicate removal, but I don't know if it is really properly testing the functionality. Also, it didn't create some of the output files specified in the command line. Perhaps with other input it would.