Change default validation stringency to SILENT and make common option… #793
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…s more easily accessible at runtime.
tfenne
commented
Feb 27, 2022
| class FgBioCommonArgs | ||
| ( @arg(doc="Use asynchronous I/O where possible, e.g. for SAM and BAM files.") val asyncIo: Boolean = false, | ||
| @arg(doc="Default GZIP compression level, BAM compression level.") val compression: Int = 5, | ||
| @arg(doc="Directory to use for temporary files.") val tmpDir: DirPath = Paths.get(System.getProperty("java.io.tmpdir")), | ||
| @arg(doc="Minimum severity log-level to emit.") val logLevel: LogLevel = LogLevel.Info, | ||
| @arg(doc="Validation stringency for SAM/BAM reading.") val samValidationStringency: Option[ValidationStringency] = None | ||
| @arg(doc="Validation stringency for SAM/BAM reading.") val samValidationStringency: ValidationStringency = ValidationStringency.STRICT |
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I'm tired of paying an extra 50% for HTSJDK to run decoding and validation when it's not needed. Thoughts?
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I agree. So do we want silent instead of strict?
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Whoopsie, silly autocomplete. Yes we do.
Codecov Report
@@ Coverage Diff @@
## master #793 +/- ##
==========================================
- Coverage 95.47% 95.45% -0.02%
==========================================
Files 121 121
Lines 6866 6870 +4
Branches 452 464 +12
==========================================
+ Hits 6555 6558 +3
- Misses 311 312 +1
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|
nh13
requested changes
Feb 27, 2022
| class FgBioCommonArgs | ||
| ( @arg(doc="Use asynchronous I/O where possible, e.g. for SAM and BAM files.") val asyncIo: Boolean = false, | ||
| @arg(doc="Default GZIP compression level, BAM compression level.") val compression: Int = 5, | ||
| @arg(doc="Directory to use for temporary files.") val tmpDir: DirPath = Paths.get(System.getProperty("java.io.tmpdir")), | ||
| @arg(doc="Minimum severity log-level to emit.") val logLevel: LogLevel = LogLevel.Info, | ||
| @arg(doc="Validation stringency for SAM/BAM reading.") val samValidationStringency: Option[ValidationStringency] = None | ||
| @arg(doc="Validation stringency for SAM/BAM reading.") val samValidationStringency: ValidationStringency = ValidationStringency.STRICT |
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I agree. So do we want silent instead of strict?
nh13
approved these changes
Feb 28, 2022
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…s more easily accessible at runtime.