implement viterbi encoding

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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implement viterbi encoding #305

Closed shajoezhu closed 5 years ago

shajoezhu commented 5 years ago

Rasie an issue before pull request, and use "#" to link to issue

see #250

List all of the key changes

implementing, taking max at forward posterior probabilities and encode to viterbi state

After this pull request, what is going to be changed?

tmp

coveralls commented 5 years ago

Pull Request Test Coverage Report for Build 933

0 of 0 changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-0.4%) to 83.763%

Totals
Change from base Build 924:	-0.4%
Covered Lines:	2373
Relevant Lines:	2833

💛 - Coveralls

shajoezhu commented 5 years ago

Much improved by setting the parameter G low

dEploid -ref PM0007-C_ref.txt -alt PM0007-C_alt.txt -plaf africaGroup3_PLAF.txt -exclude africaGroup3_and_pf3k_bad_snp_in_at_least_50_samples.txt -noPanel -ibdViterbi -initialP 0.2 0.8 -o viterbi-G0dot05 -G 0.05 dEploid -ref PM0007-C_ref.txt -alt PM0007-C_alt.txt -plaf africaGroup3_PLAF.txt -exclude africaGroup3_and_pf3k_bad_snp_in_at_least_50_samples.txt -noPanel -ibdPainting -initialP 0.2 0.8 -o ibdpost-G0dot05 -G 0.05

tmp-g0dot05