Missing parsers for command line tools

kunalkathuria / SVXplorer

Structural Variant Caller

MIT License

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Missing parsers for command line tools #85

Closed sienkie closed 4 years ago

sienkie commented 4 years ago

Currently, three scripts (calcConflict.py, vcftoBedpr.py, vcftoBed.py) in "src" directory are using sys.argv instead of argparser. Parsers need to be implemented or entire scripts removed along with corresponding lines in setup.py (these seem to be utility scripts, the implemented functions are not used in other parts of SVXplorer).

(Marked with #TODOs in both setup.py and individual scripts on pypi_release branch)

sienkie commented 4 years ago

The same goes for markLikelyConflicts.py. Currently, it does not work because of usage of both argparser and sys.argv. This script is probably not needed as it seems to contain functions that are duplicated in other parts of code.