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[ADAM-2039] Adding support for writing BED format per UCSC definition #2042

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merged 2 commits into from Oct 16, 2018

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@heuermh
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heuermh commented Sep 4, 2018

Fixes #2039

@benwbooth Please let me know if this helps.

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coveralls commented Sep 4, 2018

Coverage Status

Coverage decreased (-0.02%) to 79.055% when pulling 3666087 on heuermh:ucsc-bed-format into 3542342 on bigdatagenomics:master.

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AmplabJenkins commented Sep 4, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2801/

Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2042/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains e1d4f1f # timeout=10Checking out Revision e1d4f1f (origin/pr/2042/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f e1d4f1f0abb3cf5b75b6996a9007e2bc152ce02aFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.7.3,2.11,2.2.2,ubuntuTriggering ADAM-prb ? 2.6.2,2.11,2.2.2,ubuntuADAM-prb ? 2.7.3,2.11,2.2.2,ubuntu completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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heuermh commented Sep 4, 2018

Jenkins, retest this please

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AmplabJenkins commented Sep 4, 2018

Test PASSed.
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Test PASSed.

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fnothaft left a comment

Small nits, otherwise LGTM.

def saveAsUcscBed(fileName: String,
asSingleFile: Boolean = false,
disableFastConcat: Boolean = false,
minimumScore: Double,

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fnothaft Sep 6, 2018

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If these are "interpolated to 0/1000", shouldn't 0.0/1000.0 be the default values?

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heuermh Sep 6, 2018

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minimumScore is the score which interpolates to 0. maximumScore is the score which interpolates to 1000. Output in this convention is always integers between 0 and 1000, inclusive.

targetMin: Double,
targetMax: Double): Double = {

val v = constrain(value, sourceMin, sourceMax)

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@fnothaft

fnothaft Sep 6, 2018

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I would remove the constrain function, import scala.math.{max, min} and val v = max(min(sourceMax, value), sourceMin)

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@heuermh

@heuermh heuermh added this to the 0.24.1 milestone Sep 6, 2018

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AmplabJenkins commented Sep 6, 2018

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2803/
Test PASSed.

@fnothaft fnothaft merged commit f8304bd into bigdatagenomics:master Oct 16, 2018

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@heuermh heuermh deleted the heuermh:ucsc-bed-format branch Oct 17, 2018

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heuermh commented Oct 17, 2018

Thank you, @fnothaft

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