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Change default validation stringency to SILENT and make common option… #793

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merged 2 commits into from
Mar 1, 2022
Merged

Change default validation stringency to SILENT and make common option… #793

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0e445b0
Change default validation stringency to SILENT and make common option…
tfenne Feb 27, 2022
0e46efc
Fixup
tfenne Feb 28, 2022
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18 changes: 16 additions & 2 deletions src/main/scala/com/fulcrumgenomics/cmdline/FgBioMain.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -56,12 +56,25 @@ object FgBioMain {
case class FailureException private[cmdline] (exit: Int = 1, message: Option[String] = None) extends RuntimeException
}

/** Public object that holds a singleton instance of the common args so that it can be accessed elsewhere. */
object FgBioCommonArgs {
private var _args: FgBioCommonArgs = new FgBioCommonArgs()

/** Setter that is private to the cmdline package. */
private[cmdline] def args_=(args: FgBioCommonArgs): Unit = {
this._args = args
}

/** Access the common args for a command line program. */
def args: FgBioCommonArgs = this._args
}

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.SILENT
) {

SamSource.DefaultUseAsyncIo = asyncIo
Expand All @@ -78,7 +91,7 @@ class FgBioCommonArgs

Logger.level = this.logLevel

samValidationStringency.foreach { stringency => SamSource.DefaultValidationStringency = stringency }
SamSource.DefaultValidationStringency = samValidationStringency
}

class FgBioMain extends LazyLogging {
Expand All @@ -104,6 +117,7 @@ class FgBioMain extends LazyLogging {
case Sopt.CommandSuccess(cmd) =>
unreachable("CommandSuccess should never be returned by parseCommandAndSubCommand.")
case Sopt.SubcommandSuccess(commonArgs, subcommand) =>
FgBioCommonArgs.args = commonArgs
val name = subcommand.getClass.getSimpleName
try {
printStartupLines(name, args, commonArgs)
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