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add validation stringency to bam parsing, flagstat #976

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merged 1 commit into from Mar 24, 2016

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ryan-williams commented Mar 24, 2016

fixes #973

@@ -41,6 +41,8 @@ class FlagStatArgs extends Args4jBase with ParquetArgs {
val inputPath: String = null
@Argument(required = false, metaVar = "OUTPUT", usage = "Optionally write the stats to this file.", index = 1)
val outputPath: String = null
@Args4jOption(required = false, name = "-stringency", usage = "Set the parsing stringency: SILENT, LENIENT, STRICT.")
val stringency: String = "SILENT"

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@heuermh

heuermh Mar 24, 2016

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what is the default if SAMHeaderReader.VALIDATION_STRINGENCY_PROPERTY is not set?

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heuermh Mar 24, 2016

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what is the default if SAMHeaderReader.VALIDATION_STRINGENCY_PROPERTY is not set?

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@ryan-williams

ryan-williams Mar 24, 2016

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STRICT. flagstat is a simple enough operation that i thought SILENT was more often than not what a user would want.

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ryan-williams Mar 24, 2016

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STRICT. flagstat is a simple enough operation that i thought SILENT was more often than not what a user would want.

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@heuermh

heuermh Mar 24, 2016

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ok, I agree with you on flagstat defaulting to SILENT, and I see the default in loadBam is STRICT. +1

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heuermh Mar 24, 2016

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ok, I agree with you on flagstat defaulting to SILENT, and I see the default in loadBam is STRICT. +1

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AmplabJenkins Mar 24, 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/1112/
Test PASSed.

AmplabJenkins commented Mar 24, 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/1112/
Test PASSed.

@heuermh heuermh merged commit 9246472 into master Mar 24, 2016

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heuermh commented Mar 24, 2016

Thanks @ryan-williams!

@fnothaft fnothaft deleted the flagstat-stringency branch Nov 15, 2016

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