DEploid-dev / DEploid

dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.
http://deploid.readthedocs.io/en/latest/index.html
GNU General Public License v3.0
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Lasso before ibd #282

Closed shajoezhu closed 5 years ago

shajoezhu commented 6 years ago

need to check all the existing test for flag conflicts

coveralls commented 5 years ago

Pull Request Test Coverage Report for Build 896


Changes Missing Coverage Covered Lines Changed/Added Lines %
src/mcmc.cpp 46 51 90.2%
src/vcfReader.cpp 0 14 0.0%
src/chooseK.cpp 1 34 2.94%
src/variantIndex.cpp 0 42 0.0%
src/panel.cpp 3 51 5.88%
src/dEploidIO.cpp 17 114 14.91%
<!-- Total: 75 314 23.89% -->
Files with Coverage Reduction New Missed Lines %
src/lasso/src/dEploidLasso.cpp 1 0.0%
src/ibd.cpp 2 0.0%
src/variantIndex.cpp 3 0.0%
src/utility.cpp 5 0.0%
src/lasso/src/lasso.hpp 6 0.0%
src/exceptions.hpp 9 0.0%
src/mcmc.cpp 18 0.0%
src/vcfReader.cpp 19 0.0%
src/lasso/src/lasso.cpp 29 0.0%
src/updateHap.cpp 32 0.0%
<!-- Total: 204 -->
Totals Coverage Status
Change from base Build 878: -7.5%
Covered Lines: 2363
Relevant Lines: 2806

💛 - Coveralls