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IntelliJ ate my import!

This commit is contained in:
Mauricio Carneiro 2012-01-23 21:46:45 -05:00
parent 2bb9525e7f
commit 945cf03889
1 changed files with 3 additions and 2 deletions
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5
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
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@ -6,6 +6,7 @@ import net.sf.samtools.SAMFileHeader.SortOrder
import org.broadinstitute.sting.utils.exceptions.UserException
import org.broadinstitute.sting.commandline.Hidden
import org.broadinstitute.sting.queue.extensions.picard.{ReorderSam, SortSam, AddOrReplaceReadGroups}
import org.broadinstitute.sting.queue.extensions.gatk._
/**
* Created by IntelliJ IDEA.
@ -99,9 +100,9 @@ class PacbioProcessingPipeline extends QScript {
val bam = if (BLASR_BAM) {mqBAM} else {bamBase}
add(cov(bam, recalFile1),
add(cov(bam, recalFile1, resetQuals),
recal(bam, recalFile1, recalBam),
cov(recalBam, recalFile2, resetQuals),
cov(recalBam, recalFile2, false),
analyzeCovariates(recalFile1, path1),
analyzeCovariates(recalFile2, path2))
}