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cbg-ethz / haploclique

Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.
GNU General Public License v3.0
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options handling change #57

Closed DrYak closed 6 years ago

DrYak commented 6 years ago

This branches contains 2 different modifications to haploclique :

docopt

I've replaced the built-in docopt version 0.6.1 with an external git submodule pulling version 0.6.2.

That version contains bugfixes that cause the exceptions thrown to disappear. It also has an officially supported switch (-DUSE_BOOST_REGEX) that replace the C++11 std::regex engine with Boost.Regex, for older version like GCC 4.8.x that lack functionnal Regex.

help return code

I turned on docopt's support for --help (and --version) so that now these display the info and return a success exit code (which is a requirement for bioconda recipes' test: sections)

DrYak commented 6 years ago

@armintoepfer : oops, something is wrong Circleci doesn't even start!?

DrYak commented 6 years ago

@SoapZA : If you would also like to review this pull.

DrYak commented 6 years ago

This pull request did also happen to solve this issue regarding using upstream docopt as a submodule (done in this commit )