From f4463d38ca28209ad59b3c5cb7579c3f104fab5c Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Thu, 30 Jun 2011 14:29:21 -0400
Subject: [PATCH] BWA requires pair ended reads to be sorted by read names when
 operating over BAM files, but Picard sorts by coordinate, so in case we use
 BWA in pair ended reads, the pipeline now resorts the BAM in read name order,
 realigns it then sorts it in coordinate order.

---
 .../queue/qscripts/DataProcessingPipeline.scala | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

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 fdde5e8a2..623181de6 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
@@ -4,12 +4,12 @@ import org.broadinstitute.sting.queue.extensions.gatk._
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.function.ListWriterFunction
 
-import net.sf.samtools.{SAMFileReader,SAMReadGroupRecord}
-
 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.SAMFileHeader.SortOrder
 
 
 class DataProcessingPipeline extends QScript {
@@ -180,6 +180,7 @@ class DataProcessingPipeline extends QScript {
     var realignedBams: List[File] = List()
     var index = 1
     for (bam <- bams) {
+      val readSortedBam = swapExt(bam, ".bam", "." + index + ".sorted.bam" )
       val saiFile1 = swapExt(bam, ".bam", "." + index + ".1.sai")
       val saiFile2 = swapExt(bam, ".bam", "." + index + ".2.sai")
       val realignedSamFile = swapExt(bam, ".bam", "." + index + ".realigned.sam")
@@ -190,11 +191,12 @@ class DataProcessingPipeline extends QScript {
             bwa_sam_se(bam, saiFile1, realignedSamFile))
       }
       else {
-        add(bwa_aln_pe(bam, saiFile1, 1),
-            bwa_aln_pe(bam, saiFile2, 2),
-            bwa_sam_pe(bam, saiFile1, saiFile2, realignedSamFile))
+        add(sortSam(bam, readSortedBam, SortOrder.queryname),
+            bwa_aln_pe(readSortedBam, saiFile1, 1),
+            bwa_aln_pe(readSortedBam, saiFile2, 2),
+            bwa_sam_pe(readSortedBam, saiFile1, saiFile2, realignedSamFile))
       }
-      add(sortSam(realignedSamFile, realignedBamFile))
+      add(sortSam(realignedSamFile, realignedBamFile, SortOrder.coordinate))
       addReadGroups(realignedBamFile, rgRealignedBamFile, new SAMFileReader(bam))
       realignedBams :+= rgRealignedBamFile
       index = index + 1
@@ -385,9 +387,10 @@ class DataProcessingPipeline extends QScript {
     this.jobName = queueLogDir + outBam + ".joinBams"
   }
 
-  case class sortSam (inSam: File, outBam: File) extends SortSam {
+  case class sortSam (inSam: File, outBam: File, sortOrderP: SortOrder) extends SortSam {
     this.input = List(inSam)
     this.output = outBam
+    this.sortOrder = sortOrderP
     this.memoryLimit = 4
     this.isIntermediate = true
     this.analysisName = queueLogDir + outBam + ".sortSam"