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Expose sorting option in IlluminaBasecallsToSam #389

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May 21, 2021
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Expose sorting option in IlluminaBasecallsToSam #389

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4 changes: 3 additions & 1 deletion tasks/src/main/scala/dagr/tasks/picard/IlluminaBasecallsToSam.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,8 @@ class IlluminaBasecallsToSam(basecallsDir: DirPath,
maxReadsInRamPerTile: Option[Int] = Some(500000),
firstTile: Option[Int] = None,
tileLimit: Option[Int] = None,
tmpDir: Option[DirPath] = None
tmpDir: Option[DirPath] = None,
sort: Option[Boolean] = None
) extends PicardTask with VariableResources with JvmRanOutOfMemory {

protected val byMemoryPerThread: Memory = Memory("1GB")
Expand Down Expand Up @@ -88,6 +89,7 @@ class IlluminaBasecallsToSam(basecallsDir: DirPath,
buffer += "READ_STRUCTURE=" + readStructure.toString
buffer += "LIBRARY_PARAMS=" + libraryParamsFile
buffer += "INCLUDE_NON_PF_READS=" + includeNonPfReads
sort.foreach(buffer += "SORT=" + _)
if (ignoreUnexpectedBarcodes) buffer += "IGNORE_UNEXPECTED_BARCODES=true"
if (adapterPairs.isEmpty) buffer += "ADAPTERS_TO_CHECK=null"
else adapterPairs.foreach(buffer += "ADAPTERS_TO_CHECK=" + _)
Expand Down