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broadinstitute / gamgee

A C++14 library for NGS data formats
http://broadinstitute.github.io/gamgee/
MIT License
40 stars 13 forks source link

Fix for https://github.com/broadinstitute/foghorn/issues/149 #385

Closed kgururaj closed 9 years ago

kgururaj commented 9 years ago

Fix for https://github.com/broadinstitute/foghorn/issues/149 Check for missing variant in MultipleVariantIterator - important if one of the inputs is a blank VCF TODO: Are there other places this check needs to be done?

droazen commented 9 years ago

Let's hold off on merging this fix until https://github.com/broadinstitute/gamgee/pull/384 is merged, as it conflicts with the changes in that branch.

coveralls commented 9 years ago

Coverage Status

Coverage increased (+4.47%) when pulling 92e28affe1382a442d66f36494b125a6cae1e959 on intel_multi_iterator_fix into a25b637cdba32d3ade0dafc9f5f76ee7b443e051 on master.

droazen commented 9 years ago

Now that https://github.com/broadinstitute/gamgee/pull/384 has been merged, this can be rebased on top of those changes (will probably get merge conflicts).

jmthibault79 commented 9 years ago

I would like to see a test which demonstrates the fix as well.

Thanks for looking into this btw!

droazen commented 9 years ago

What is the status of this?

kgururaj commented 9 years ago

Added a test case for empty VCF traversal using MVI. The test crashes without the fix.

coveralls commented 9 years ago

Coverage Status

Coverage increased (+0.01%) when pulling 6ce944371987567014d4b327a273b231d389eb44 on intel_multi_iterator_fix into cc0a9d2f4eb37412ab8a98c2f0d1be6bab798b2f on master.

droazen commented 9 years ago

:+1: looks good to me -- but @jmthibault79 should have a look too

jmthibault79 commented 9 years ago

Looks good but I would also like a copy of the test for MultipleVariantIterator (current one tests ReferenceBlockSplittingVariantIterator). OK to rebase and merge yourself when that is added.

coveralls commented 9 years ago

Coverage Status

Coverage increased (+0.01%) when pulling 5b0e0f9b44c743917291a4c6d3070736196906c3 on intel_multi_iterator_fix into a2a227b188654b8a495eee5e88177ef3fb11632a on master.