From 945cf038895d930705bfa80cf80ab8e2c0de6743 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Mon, 23 Jan 2012 21:46:45 -0500 Subject: [PATCH] IntelliJ ate my import! --- .../sting/queue/qscripts/PacbioProcessingPipeline.scala | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala index 5cbea8ac4..d5f7512e4 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala @@ -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)) }