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error in compilation of SortSam using Queue

I have been trying to run SortSam using Queue on my data (using this sample code here: http://gatkforums.broadinstitute.org/gatk/discussion/3293/scala-script-for-running-queue)

When I try the dry run, I get an compilation error:

INFO 11:32:12,970 QScriptManager - Compiling 1 QScript
ERROR 11:32:14,551 QScriptManager - GATKTest2.scala:5: not found: object net
ERROR 11:32:14,553 QScriptManager - import net.sf.samtools.SAMFileHeader.SortOrder
ERROR 11:32:14,574 QScriptManager - ^
ERROR 11:32:14,721 QScriptManager - GATKTest2.scala:28: not found: type SortOrder
ERROR 11:32:14,721 QScriptManager - var sortingOrder: SortOrder = SortOrder.coordinate

I have tried the other GATK scala examples, and they all work fine. --- They work fine when I use this:
"import org.broadinstitute.gatk.queue.QScript". They don't work if I use "import org.broadinstitute.sting.queue.QScript"

Can anyone help me with this ?



Issue · Github
by Sheila

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