diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala index e62b1b926..40ac43a81 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala @@ -7,10 +7,10 @@ import org.broadinstitute.sting.queue.function.ListWriterFunction import collection.JavaConversions._ import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel import org.broadinstitute.sting.queue.extensions.picard._ -import net.sf.samtools.{SAMFileReader} +import net.sf.samtools.SAMFileReader import net.sf.samtools.SAMFileHeader.SortOrder -import org.broadinstitute.sting.queue.qscripts.utils.Utils +import org.broadinstitute.sting.queue.util.Utils class DataProcessingPipeline extends QScript { qscript => diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala index b2960f150..8ba880291 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala @@ -2,9 +2,7 @@ package org.broadinstitute.sting.queue.qscripts import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.extensions.gatk._ -import net.sf.samtools.SAMFileReader -import io.Source._ -import org.broadinstitute.sting.queue.qscripts.utils.Utils +import org.broadinstitute.sting.queue.util.Utils /** * Created by IntelliJ IDEA. diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/utils/Utils.scala b/public/scala/src/org/broadinstitute/sting/queue/util/Utils.scala similarity index 96% rename from public/scala/qscript/org/broadinstitute/sting/queue/qscripts/utils/Utils.scala rename to public/scala/src/org/broadinstitute/sting/queue/util/Utils.scala index 1189b376c..5b80503a3 100644 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/utils/Utils.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/util/Utils.scala @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.queue.qscripts.utils +package org.broadinstitute.sting.queue.util import java.io.File import io.Source._