Optionally allow duplicated mutations when using load_vcf or load_maf. Fixes #211

[tuomastik]

This change is 

[coveralls]

Coverage remained the same at 88.582% when pulling 46ed6b4 on tuomastik:allow_duplicated_mutations into c0fcf14 on hammerlab:master.

[iskandr]

Looks like this failed on Travis because of unrelated (need to install Ensembl 87 on travis), I'll fix that shortly and re-run your tests.

[coveralls]

Coverage remained the same at 88.218% when pulling 22dcb0f on tuomastik:allow_duplicated_mutations into 97c7a2b on hammerlab:master.

[iskandr]

Hey @tuomastik I merged your other PR and I think that created merge conflicts with this one. I also moved the confusing sort order of VariantCollection to a separate issue. Thanks for these PRs! Sorry I've been slow in getting to them.

[tuomastik]

Thanks @iskandr and no worries about the time taken! I just resolved the conflicts with the base branch.

[coveralls]

Coverage remained the same at 88.218% when pulling 3322533 on tuomastik:allow_duplicated_mutations into 189ba0b on hammerlab:master.

[coveralls]

Coverage remained the same at 87.294% when pulling a5a8d16 on tuomastik:allow_duplicated_mutations into 6a97720 on hammerlab:master.

[iskandr]

Hey @tuomastik, I'll update the Varcode version on PyPI later today, thanks for the PR!