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Squashed #907 and ran format-sources #908

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merged 1 commit into from Jan 7, 2016

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fnothaft commented Jan 7, 2016

This PR contains the changes from #907 by @huitseeker squashed down to a single commit. After squashing down, I ran ./scripts/format-source, which should resolve the Jenkins failure we're seeing on #907. I'm opening this as a new PR to get @AmplabJenkins to retest it.

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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1042/
Test PASSed.

AmplabJenkins commented Jan 7, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1042/
Test PASSed.

@fnothaft fnothaft added this to the 0.19.0 milestone Jan 7, 2016

Fix various minor code issues:
* disuse of builtin functions for common reduce operations
* unneceessary toString
* risky/anti-idiomatic Option usage
* Cleaning up TODOs in Vcfutils
* retire VcfStringUtils
* finer exception types in some places
* more explicit Fastq error message in stringent mode
* allow IUPAC codes as isRegularBase alternatives
* Add debug output for Fastq record
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fnothaft Jan 7, 2016

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I've just squashed the commits down.

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fnothaft commented Jan 7, 2016

I've just squashed the commits down.

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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1043/
Test PASSed.

AmplabJenkins commented Jan 7, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1043/
Test PASSed.

heuermh added a commit that referenced this pull request Jan 7, 2016

@heuermh heuermh merged commit af778e0 into bigdatagenomics:master Jan 7, 2016

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heuermh commented Jan 7, 2016

Thank you @fnothaft @huitseeker!

@heuermh heuermh referenced this pull request Jan 7, 2016

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Various small fixes #907

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