Fixing conflicts.

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala

@@ -4,13 +4,13 @@ import org.broadinstitute.sting.queue.extensions.gatk._
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.function.ListWriterFunction
 
-import scala.io.Source._
 import collection.JavaConversions._
 import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel
 import org.broadinstitute.sting.queue.extensions.picard._
-import net.sf.samtools.{SAMFileReader, SAMReadGroupRecord}
+import net.sf.samtools.{SAMFileReader}
 import net.sf.samtools.SAMFileHeader.SortOrder
 
+import org.broadinstitute.sting.queue.qscripts.utils.Utils
 
 class DataProcessingPipeline extends QScript {
   qscript =>
@@ -103,18 +103,6 @@ class DataProcessingPipeline extends QScript {
                    val ds: String)
   {}
 
-  // Utility function to check if there are multiple samples in a BAM file (currently we can't deal with that)
-  def hasMultipleSamples(readGroups: java.util.List[SAMReadGroupRecord]): Boolean = {
-    var sample: String = ""
-    for (r <- readGroups) {
-      if (sample.isEmpty)
-        sample = r.getSample
-      else if (sample != r.getSample)
-          return true;
-    }
-    return false
-  }
-
   // Utility function to merge all bam files of similar samples. Generates one BAM file per sample.
   // It uses the sample information on the header of the input BAM files.
   //
@@ -135,7 +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(!hasMultipleSamples(readGroups), "The pipeline requires that only one sample is present in a BAM file. Please separate the samples in " + bam)
+      assert(!Utils.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) {
@@ -166,12 +154,6 @@ class DataProcessingPipeline extends QScript {
     return sampleBamFiles.toMap
   }
 
-  // Checks how many contigs are in the dataset. Uses the BAM file header information.
-  def getNumberOfContigs(bamFile: File): Int = {
-    val samReader = new SAMFileReader(new File(bamFile))
-    return samReader.getFileHeader.getSequenceDictionary.getSequences.size()
-  }
-
   // Rebuilds the Read Group string to give BWA
   def addReadGroups(inBam: File, outBam: File, samReader: SAMFileReader) {
     val readGroups = samReader.getFileHeader.getReadGroups
@@ -215,19 +197,6 @@ class DataProcessingPipeline extends QScript {
     return realignedBams
   }
 
-  // Reads a BAM LIST file and creates a scala list with all the files
-  def createListFromFile(in: File):List[File] = {
-    if (in.toString.endsWith("bam"))
-      return List(in)
-    var l: List[File] = List()
-    for (bam <- fromFile(in).getLines) {
-      if (!bam.startsWith("#") && !bam.isEmpty)
-        l :+= new File(bam.trim)
-    }
-    return l
-  }
-
-
 
   /****************************************************************************
   * Main script
@@ -237,8 +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 = createListFromFile(input)
+    val bams = Utils.createListFromFile(input)
-    nContigs = getNumberOfContigs(bams(0))
+    nContigs = Utils.getNumberOfContigs(bams(0))
 
     val realignedBams = if (useBWApe || useBWAse) {performAlignment(bams)} else {bams}
 

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala

@@ -4,6 +4,7 @@ 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
 
 /**
  * Created by IntelliJ IDEA.
@@ -33,25 +34,10 @@ class RecalibrateBaseQualities extends QScript {
   val queueLogDir: String = ".qlog/"
   var nContigs: Int = 0
 
-  def getNumberOfContigs(bamFile: File): Int = {
-    val samReader = new SAMFileReader(new File(bamFile))
-    return samReader.getFileHeader.getSequenceDictionary.getSequences.size()
-  }
-
-  // Reads a BAM LIST file and creates a scala list with all the files
-  def createListFromFile(in: File):List[File] = {
-    if (in.toString.endsWith("bam"))
-      return List(in)
-    var l: List[File] = List()
-    for (bam <- fromFile(in).getLines)
-      l :+= new File(bam)
-    return l
-  }
-
   def script = {
 
-    val bamList = createListFromFile(input)
+    val bamList = Utils.createListFromFile(input)
-    nContigs = getNumberOfContigs(bamList(0))
+    nContigs = Utils.getNumberOfContigs(bamList(0))
 
     for (bam <- bamList) {
 

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/utils/Utils.scala

@@ -0,0 +1,60 @@
+package org.broadinstitute.sting.queue.qscripts.utils
+
+import java.io.File
+import io.Source._
+import net.sf.samtools.{SAMReadGroupRecord, SAMFileReader}
+
+import collection.JavaConversions._
+
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: carneiro
+ * Date: 7/14/11
+ * Time: 4:57 PM
+ * To change this template use File | Settings | File Templates.
+ */
+
+object Utils {
+
+  /**
+   * Takes a bam list file and produces a scala list with each file allowing the bam list
+   * to have empty lines and comment lines (lines starting with #).
+   */
+  def createListFromFile(in: File):List[File] = {
+    // If the file provided ends with .bam, it is not a bam list, we treat it as a single file.
+    // and return a list with only this file.
+    if (in.toString.endsWith(".bam"))
+      return List(in)
+
+    var list: List[File] = List()
+    for (bam <- fromFile(in).getLines)
+      if (!bam.startsWith("#") && !bam.isEmpty )
+        list :+= new File(bam.trim())
+    list
+  }
+
+  /**
+   * Returns the number of contigs in the BAM file header.
+   */
+  def getNumberOfContigs(bamFile: File): Int = {
+    val samReader = new SAMFileReader(new File(bamFile))
+    samReader.getFileHeader.getSequenceDictionary.getSequences.size()
+  }
+
+  /**
+   * Check if there are multiple samples in a BAM file
+   */
+  def hasMultipleSamples(readGroups: java.util.List[SAMReadGroupRecord]): Boolean = {
+    var sample: String = ""
+    for (r <- readGroups) {
+      if (sample.isEmpty)
+        sample = r.getSample
+      else if (sample != r.getSample)
+          return true;
+    }
+    false
+  }
+
+
+}