VerifyBamId update - Githubissues

googlegenomics / dataflow-java

Google Cloud Dataflow pipelines such as Identity-By-State as well as useful utility classes.

Apache License 2.0

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VerifyBamId update #210

Closed sergipv closed 8 years ago

sergipv commented 8 years ago

Pipeline was not working for a couple of reasons:

AlleleFreq and ReadBaseQuality had a Coder that was not working (updated to AvroCoder).
AlleleFreq had no numerical value populated but a string value.

Updated the tests (basically failing because ContainsInAnyOrder was expected all KV<Position, ReadCount> and not only one.

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coveralls commented 8 years ago

Coverage increased (+1.8%) to 21.615% when pulling ca67c95ee08d98b64ee48b208aec8078b9b8a55d on sergipv:master into fe02a0745525ecbc3bb5077cf3fa321435a22765 on googlegenomics:master.

coveralls commented 8 years ago

Coverage increased (+1.8%) to 21.615% when pulling ca67c95ee08d98b64ee48b208aec8078b9b8a55d on sergipv:master into fe02a0745525ecbc3bb5077cf3fa321435a22765 on googlegenomics:master.

coveralls commented 8 years ago

Coverage increased (+1.8%) to 21.615% when pulling be13fbfdfd4ec884383362f06d2efeeda3005aeb on sergipv:master into fe02a0745525ecbc3bb5077cf3fa321435a22765 on googlegenomics:master.

coveralls commented 8 years ago

Coverage increased (+1.8%) to 21.615% when pulling be13fbfdfd4ec884383362f06d2efeeda3005aeb on sergipv:master into fe02a0745525ecbc3bb5077cf3fa321435a22765 on googlegenomics:master.

coveralls commented 8 years ago

Coverage increased (+1.8%) to 21.615% when pulling be13fbfdfd4ec884383362f06d2efeeda3005aeb on sergipv:master into fe02a0745525ecbc3bb5077cf3fa321435a22765 on googlegenomics:master.

deflaux commented 8 years ago

@sergipv these are great fixes - thank you!!!

Just a nit, it looks like some of the white space is a bit off in the diff. Our goal is to follow the Google Java Style Guide.

Can you please update the spacing? Otherwise this looks good to me!

coveralls commented 8 years ago

Coverage increased (+1.8%) to 21.615% when pulling 0ac75e24a1ed302e4148bfcebd27975af10c2d6e on sergipv:master into fe02a0745525ecbc3bb5077cf3fa321435a22765 on googlegenomics:master.

coveralls commented 8 years ago

Coverage increased (+1.8%) to 21.615% when pulling 0ac75e24a1ed302e4148bfcebd27975af10c2d6e on sergipv:master into fe02a0745525ecbc3bb5077cf3fa321435a22765 on googlegenomics:master.

coveralls commented 8 years ago

Coverage increased (+1.8%) to 21.599% when pulling 9402b10995b23ba57c16956aef3047afc1a4e3af on sergipv:master into fe02a0745525ecbc3bb5077cf3fa321435a22765 on googlegenomics:master.

coveralls commented 8 years ago

Coverage increased (+1.8%) to 21.599% when pulling 94d7e49e8356f749877bbf20754bb43b1c44d2f0 on sergipv:master into fe02a0745525ecbc3bb5077cf3fa321435a22765 on googlegenomics:master.

sergipv commented 8 years ago

@deflaux, changes done! My local vim screwed up the spacing and I didn't review it in github. Let me know if you see anything off (I reviewed a couple of times but maybe I am missing something).

coveralls commented 8 years ago

Coverage increased (+1.8%) to 21.599% when pulling c0a4c680e0322d4f54a258f0361833caec2ef15d on sergipv:master into fe02a0745525ecbc3bb5077cf3fa321435a22765 on googlegenomics:master.

deflaux commented 8 years ago

@sergipv thanks for fixing https://github.com/googlegenomics/dataflow-java/issues/155 !!