broadinstitute / oncotator / 467

66%

push

travis-ci

Issue 343 fix ex ac ds (#344)

* Changes to accommodate the new pyVCF.  Upgrading pysam.  Still need to update build scripts.  Also, accommodating new missing format field convention (if it is missing, annotate w/ "")

* Updates to support new version of COSMIC and updating automated tests.  Additionally, more updates to support ExAC VCF.

* Updates to make preprocessing of cosmic data faster and correct with new headers, etc in COSMIC v76

* Fixing bufcount rename

* Fixing -w not being honored for VCF input

* Fixing unit test setup failure (hopefully)

* Undoing previous commit

* Updating pysam version in dockerfile and eliminating dependency on other fork of pyvcf

* Pegging python version in travis yml and docker.  Should fix issue with distribute.  Not a long-term solution... Since it means that oncotator onlyu works on python 2.7.9 and below.

* Eliminating trailing comma in setup that was causing grief on specific platforms

* Testing another thing for travis.

* Attempting to fix travis (and docker) by eliminating the deprecated distribute package.

* Fixing issue with _io.BytesIO does not have name attribute (!)

* Addressing PR comment regarding pegging versions of packages.

* Addressing PR comments and deleting oncotator-annotate.py, since that is a relic of bygone years.

* Looks like VCF writer does not support ``with`` blocks.

134 of 134 new or added lines in 13 files covered. (100.0%)

10816 of 16476 relevant lines covered (65.65%)

0.66 hits per line