add validation stringency to bam parsing, flagstat #976
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| @@ -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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what is the default if SAMHeaderReader.VALIDATION_STRINGENCY_PROPERTY is not set?
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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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ok, I agree with you on flagstat defaulting to SILENT, and I see the default in loadBam is STRICT. +1
|
Test PASSed. |
|
Thanks @ryan-williams! |
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fixes #973