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Refactoring Qscript utils into queue general utils package.

This commit is contained in:
Mauricio Carneiro 2011-07-15 14:31:43 -04:00
parent 43c6a8565b
commit a670d6420a
3 changed files with 4 additions and 6 deletions
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4
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -7,10 +7,10 @@ import org.broadinstitute.sting.queue.function.ListWriterFunction
import collection.JavaConversions._ import collection.JavaConversions._
import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel
import org.broadinstitute.sting.queue.extensions.picard._ import org.broadinstitute.sting.queue.extensions.picard._
import net.sf.samtools.{SAMFileReader} import net.sf.samtools.SAMFileReader
import net.sf.samtools.SAMFileHeader.SortOrder 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 { class DataProcessingPipeline extends QScript {
qscript => qscript =>

4
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
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@ -2,9 +2,7 @@ package org.broadinstitute.sting.queue.qscripts
import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk._
import net.sf.samtools.SAMFileReader import org.broadinstitute.sting.queue.util.Utils
import io.Source._
import org.broadinstitute.sting.queue.qscripts.utils.Utils
/** /**
* Created by IntelliJ IDEA. * Created by IntelliJ IDEA.

2
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/utils/Utils.scala → public/scala/src/org/broadinstitute/sting/queue/util/Utils.scala
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.queue.qscripts.utils package org.broadinstitute.sting.queue.util
import java.io.File import java.io.File
import io.Source._ import io.Source._