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hammerlab / guacamole

Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly
Apache License 2.0
84 stars 21 forks source link

Merge master into hbupgrade, resolving conflicts, and add a couple things #578

Closed ryan-williams closed 8 years ago

ryan-williams commented 8 years ago

After our success with PR-on-PR reviews last week, I took an extra leap here and am resolving merge conflicts on #569 with this PR (as well as touching up a couple of things).

Unfortunately, it looks like github is presenting that in way that requires some inspection to grok:

Only the last two commits here are significant novel: https://github.com/hammerlab/guacamole/commit/5e1120d5e595da9d7f327b49fa4f0b41fffbf79a (merge master into this branch to resolve conflicts) and https://github.com/hammerlab/guacamole/commit/1c99dd04278ad5942aa046cad165fbc3648e7d00 (a few touch-ups I decided to add), but it's also showing all the commits from master that branch hbupgrade doesn't yet include, since technically those will become part of hbupgrade if we merge them in this way (as opposed to rebasing+force-pushing hbupgrade).

After merging this in to #569, those two, plus the existing #569 commits, are all that will exist as part of that PR; a nice clean view of that is here: https://github.com/hammerlab/guacamole/compare/master...ryan-williams:hbu?expand=1, comparing this branch (ryan-williams/hbu) to master.

In any case, if you'd rather not deal with that, I can make a new PR from this branch directly, or you can go resolve the conflicts yourself (via merge or rebase, your choice), and then I can send my changes on top or as a separate PR. Up to you!

This change is Reviewable

coveralls commented 8 years ago

Coverage Status

Coverage increased (+3.3%) to 78.524% when pulling 1c99dd04278ad5942aa046cad165fbc3648e7d00 on ryan-williams:hbu into 1fa0b10dc66cbd9daebaa983a28b12e270065d8c on hammerlab:hbupgrade.

arahuja commented 8 years ago

Closing this, as mentioned in #569. I re-based that branch and picked out the top commit from this.

coveralls commented 8 years ago

Coverage Status

Coverage decreased (-0.007%) to 78.602% when pulling 128812a1f9400f49fbdd94c1ad9c3a726707fa41 on ryan-williams:hbu into 9399060619e5f4f9890636f8bec3affb553c42c3 on hammerlab:hbupgrade.