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Resolving conflicts 

Conflicts:
	private/scala/qscript/depristo/ExomePostQCEval.scala
	private/scala/qscript/depristo/PostCallingQC.scala
	private/scala/qscript/org/broadinstitute/sting/queue/qscripts/archive/ExomePostQCEval.scala
This commit is contained in:
Mauricio Carneiro 2011-07-15 16:21:42 -04:00
parent ce4d702e25 210368c128
commit aa30f416a3
3 changed files with 11 additions and 13 deletions
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10
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 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.QScriptUtils
class DataProcessingPipeline extends QScript {
qscript =>
@ -123,7 +123,7 @@ class DataProcessingPipeline extends QScript {
// only allow one sample per file. Bam files with multiple samples would require pre-processing of the file
// with PrintReads to separate the samples. Tell user to do it himself!
assert(!Utils.hasMultipleSamples(readGroups), "The pipeline requires that only one sample is present in a BAM file. Please separate the samples in " + bam)
assert(!QScriptUtils.hasMultipleSamples(readGroups), "The pipeline requires that only one sample is present in a BAM file. Please separate the samples in " + bam)
// Fill out the sample table with the readgroups in this file
for (rg <- readGroups) {
@ -206,8 +206,8 @@ class DataProcessingPipeline extends QScript {
def script = {
// keep a record of the number of contigs in the first bam file in the list
val bams = Utils.createListFromFile(input)
nContigs = Utils.getNumberOfContigs(bams(0))
val bams = QScriptUtils.createListFromFile(input)
nContigs = QScriptUtils.getNumberOfContigs(bams(0))
val realignedBams = if (useBWApe || useBWAse) {performAlignment(bams)} else {bams}

8
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.extensions.gatk._
import net.sf.samtools.SAMFileReader
import io.Source._
import org.broadinstitute.sting.queue.qscripts.utils.Utils
import org.broadinstitute.sting.queue.util.QScriptUtils
/**
* Created by IntelliJ IDEA.
@ -36,8 +34,8 @@ class RecalibrateBaseQualities extends QScript {
def script = {
val bamList = Utils.createListFromFile(input)
nContigs = Utils.getNumberOfContigs(bamList(0))
val bamList = QScriptUtils.createListFromFile(input)
nContigs = QScriptUtils.getNumberOfContigs(bamList(0))
for (bam <- bamList) {

6
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/utils/Utils.scala → public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
View File

@ -1,4 +1,4 @@
package org.broadinstitute.sting.queue.qscripts.utils
package org.broadinstitute.sting.queue.util
import java.io.File
import io.Source._
@ -15,7 +15,7 @@ import collection.JavaConversions._
* To change this template use File | Settings | File Templates.
*/
object Utils {
object QScriptUtils {
/**
* Takes a bam list file and produces a scala list with each file allowing the bam list
@ -38,7 +38,7 @@ object Utils {
* Returns the number of contigs in the BAM file header.
*/
def getNumberOfContigs(bamFile: File): Int = {
val samReader = new SAMFileReader(new File(bamFile))
val samReader = new SAMFileReader(bamFile)
samReader.getFileHeader.getSequenceDictionary.getSequences.size()
}