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Fixes async io usage for picard tasks; Just realized that a non-backw…
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…ards compatible change was introduced to HTSJDK last year.
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tfenne committed May 5, 2017
1 parent af8940a commit 8f98ef6
Showing 1 changed file with 4 additions and 1 deletion.
5 changes: 4 additions & 1 deletion tasks/src/main/scala/dagr/tasks/picard/PicardTask.scala
Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,10 @@ abstract class PicardTask(var jvmArgs: List[String] = Nil,
val jvmProps = mutable.Map[String,String]()
compressionLevel.foreach(c => jvmProps("samjdk.compression_level") = c.toString)
bufferSize.foreach(b => jvmProps("samjdk.buffer_size") = b.toString)
if (useAsyncIo) jvmProps("samjdk.use_async_io") = "true"
if (useAsyncIo) {
jvmProps("samjdk.use_async_io_read_samtools") = "true"
jvmProps("samjdk.use_async_io_write_samtools") = "true"
}
buffer.appendAll(jarArgs(jarPath, jvmArgs=jvmArgs, jvmProperties=jvmProps,
jvmMemory=this.resources.memory, useAdvancedGcOptions=useAdvancedGcOptions))

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