From c3fb321014c4c1d6bd0e033d7eb7aebc91acd08f Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Tue, 22 May 2012 10:24:45 -0400
Subject: [PATCH] Minor updates to pacbio data processing script to make it
 work with the latest bwa version/settings.

---
 .../sting/queue/qscripts/PacbioProcessingPipeline.scala        | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
index c64eef7f7..46587c5b6 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
@@ -130,6 +130,7 @@ class PacbioProcessingPipeline extends QScript {
   case class sortSam (inSam: File, outBam: File) extends SortSam with ExternalCommonArgs {
     this.input = List(inSam)
     this.output = outBam
+    this.memoryLimit = 8
     this.sortOrder = SortOrder.coordinate
     this.analysisName = queueLogDir + outBam + ".sortSam"
     this.jobName = queueLogDir + outBam + ".sortSam"
@@ -171,6 +172,7 @@ class PacbioProcessingPipeline extends QScript {
     this.analysisName = queueLogDir + outRecalFile + ".covariates"
     this.jobName = queueLogDir + outRecalFile + ".covariates"
     this.scatterCount = threads
+    this.read_filter :+= "BadCigar"
   }
 
   case class recal (inBam: File, inRecalFile: File, outBam: File) extends TableRecalibration with CommandLineGATKArgs {
@@ -182,6 +184,7 @@ class PacbioProcessingPipeline extends QScript {
     this.isIntermediate = false
     this.analysisName = queueLogDir + outBam + ".recalibration"
     this.jobName = queueLogDir + outBam + ".recalibration"
+    this.read_filter :+= "BadCigar"
     this.scatterCount = threads
   }