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Validate IO in SortBam to provide nicer exceptions #994

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Jul 15, 2024
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Validate IO in SortBam to provide nicer exceptions #994

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8 changes: 5 additions & 3 deletions src/main/scala/com/fulcrumgenomics/bam/SortBam.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -59,13 +59,15 @@
@arg(flag='s', doc="Order into which to sort the records.") val sortOrder: SamOrder = SamOrder.Coordinate,
@arg(flag='m', doc="Max records in RAM.") val maxRecordsInRam: Int = SamWriter.DefaultMaxRecordsInRam
) extends FgBioTool with LazyLogging {

Io.assertReadable(input)
Io.assertCanWriteFile(output)

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Naive question, what changes when these are moved to the constructor/class body?

Since the constructor doesn't do anything else, and nothing happens in execute before the assert, I would have thought that asserting at either location would be functionally the same

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Exceptions in the constructor are ValidationExceptions, and any exceptions (typically validation errors of the arguments) are nicely formatted on the command line, versus a huge stacktrace. And it will print out the usage too. But none of those things will happen when running the tool


override def execute(): Unit = {
Io.assertReadable(input)
Io.assertCanWriteFile(output)

val in = SamSource(input)
val out = SamWriter(output, in.header.clone(), sort=Some(sortOrder), maxRecordsInRam=maxRecordsInRam)
out ++= in
out.close()
in.safelyClose()

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Also a naive question, why doesn't out also take safelyClose()?

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The idea is that we care that the output files are closed, but do not want the tool to fail/crash/except when we're cleaning up resources after the main effort of the tool has completed, so we do not propagate errors during closing inputs in this case.

}
}
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