Merge Development into master

[zeeev]

Given @skingan and @pb-cdunn testing over the last couple days, I'm comfortable merging development into master. We now have a synthetic functional test that will protect the accuracy of the algorithm.

[skingan]

We need to remove 5eba263 (Re-write emit_haplotigs.pl in Python) from development as this should be part of pb-falcon-phase not version1. I'm not sure how to do this. I think we are ready to merge to development but would like to talk to @zeeev first. I also want to test on a real dataset.

[pb-cdunn]

git revert 5eba263
git push origin development

Note that our code will diverge quickly, for a variety of reasons.

[zeeev]

Hi @pb-cdunn the command you suggested generates the following error:

To https://github.com/phasegenomics/FALCON-Phase.git ! [rejected] development -> development (non-fast-forward) error: failed to push some refs to 'https://github.com/phasegenomics/FALCON-Phase.git' hint: Updates were rejected because a pushed branch tip is behind its remote hint: counterpart. Check out this branch and integrate the remote changes hint: (e.g. 'git pull ...') before pushing again. hint: See the 'Note about fast-forwards' in 'git push --help' for details.

[pb-cdunn]

git checkout development
git pull --rebase origin development
git revert 5eba263
git push origin development