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[ADAM-1955] Add support for downsampling during recalibration table generation #1963

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merged 1 commit into from Mar 23, 2018

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fnothaft commented Mar 22, 2018

Resolves #1955.

@fnothaft fnothaft added this to the 0.24.0 milestone Mar 22, 2018

@fnothaft fnothaft requested a review from heuermh Mar 22, 2018

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AmplabJenkins commented Mar 23, 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/2736/
Test PASSed.

@Args4jOption(required = false, name = "-sampling_fraction", usage = "Fraction of reads to sample during recalibration; omitted by default.")
var samplingFraction: Double = 0.0
@Args4jOption(required = false, name = "-sampling_seed", usage = "Seed to use when sampling during recalibration; omitted by default by setting to 0 (thus, 0 is an invalid seed).")
var samplingSeed: Long = 0L

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heuermh Mar 23, 2018

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I'm not sure I get default by setting to zero, why not unspecified?

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fnothaft Mar 23, 2018

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You can't set a scala.Long to null, so you have to pick a default value (otherwise, we use null as unspecified).

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@heuermh

heuermh Mar 23, 2018

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ah ok.

@heuermh heuermh merged commit 69a8fe0 into bigdatagenomics:master Mar 23, 2018

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Codacy/PR Quality Review Not so good... This pull request quality could be better.
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heuermh commented Mar 23, 2018

Thank you, @fnothaft

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