From e2b9227d8d6629035041283bcbb57ae52b99884e Mon Sep 17 00:00:00 2001
From: carneiro <carneiro@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 3 May 2011 21:16:37 +0000
Subject: [PATCH] script to test BQSR on good/bad regions

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5743 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../oneoffs/carneiro/justRecalibrate.scala    | 116 ++++++++++++++++++
 1 file changed, 116 insertions(+)
 create mode 100755 scala/qscript/oneoffs/carneiro/justRecalibrate.scala

diff --git a/scala/qscript/oneoffs/carneiro/justRecalibrate.scala b/scala/qscript/oneoffs/carneiro/justRecalibrate.scala
new file mode 100755
index 000000000..4867bf0bd
--- /dev/null
+++ b/scala/qscript/oneoffs/carneiro/justRecalibrate.scala
@@ -0,0 +1,116 @@
+package oneoffs.carneiro
+
+import org.broadinstitute.sting.queue.QScript
+import org.broadinstitute.sting.queue.extensions.gatk._
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: carneiro
+ * Date: 4/20/11
+ * Time: 16:29 PM
+ */
+
+
+class justRecalibrate extends QScript {
+
+  @Input(doc="path to GenomeAnalysisTK.jar", shortName="gatk", required=true)
+  var GATKjar: File = _
+
+  @Input(doc="input BAM file - or list of BAM files", shortName="i", required=true)
+  var input: File = _
+
+  @Input(doc="path to AnalyzeCovariates.jar", fullName="path_to_ac_jar", shortName="ac", required=false)
+  var ACJar: File = new File("/humgen/gsa-scr1/carneiro/stable/dist/AnalyzeCovariates.jar")
+
+  @Input(doc="path to R resources folder inside the Sting repository", fullName="path_to_r", shortName="r", required=false)
+  var R: String = new File("/humgen/gsa-scr1/carneiro/stable/R")
+
+  @Input(doc="bad regions interval", shortName="bad", required=false)
+  var badInterval: File = new File("/humgen/gsa-hpprojects/dev/carneiro/goodbad/data/bad_regions.hg19.intervals")
+                                                                     
+  @Input(doc="Reference fasta file", shortName="R", required=false)
+  var reference: File = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
+
+  @Input(doc="dbsnp ROD to use (VCF)", shortName="D", required=false)
+  var dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
+
+  val queueLogDir: String = ".qlog/"
+
+
+  def script = {
+
+    val first: Boolean = true
+    val bad: Boolean = true
+
+    val badRecalFile1: File = new File("bad_recal1.csv");
+    val badRecalFile2: File = new File("bad_recal2.csv");
+    val badBam: File        = new File("bad.bam");
+    val badPath1: String    = "bad1";
+    val badPath2: String    = "bad2";
+    
+    val goodRecalFile1: File = new File("good_recal1.csv")
+    val goodRecalFile2: File = new File("good_recal2.csv")
+    val goodBam: File        = new File("good.bam")
+    val goodPath1: String    = "good1"
+    val goodPath2: String    = "good2"
+    
+    add(cov(input, badRecalFile1, first, bad),
+        recal(input, badRecalFile1, badBam, bad),
+        cov(badBam, badRecalFile2, !first, bad),
+        analyzeCovariates(badRecalFile1, badPath1),
+        analyzeCovariates(badRecalFile2, badPath2))
+
+    add(cov(input, goodRecalFile1, first, !bad),
+        recal(input, goodRecalFile1, goodBam, !bad),
+        cov(goodBam, goodRecalFile2, !first, !bad),
+        analyzeCovariates(goodRecalFile1, goodPath1),
+        analyzeCovariates(goodRecalFile2, goodPath2))
+  }
+
+  trait CommandLineGATKArgs extends CommandLineGATK {
+    this.jarFile = GATKjar
+    this.reference_sequence = reference
+    this.memoryLimit = 4
+    this.isIntermediate = true
+  }
+
+  case class cov (inBam: File, outRecalFile: File, FIRST: Boolean, BAD: Boolean) extends CountCovariates with CommandLineGATKArgs {
+    this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
+    this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
+    this.input_file :+= inBam
+    this.recal_file = outRecalFile
+    this.useOriginalQualities = FIRST
+    this.analysisName = queueLogDir + outRecalFile + ".covariates"
+    this.jobName = queueLogDir + outRecalFile + ".covariates"
+    if (BAD) {
+      this.intervals :+= badInterval
+      this.scatterCount = 85
+    }
+    else
+      this.excludeIntervals :+= badInterval
+  }
+
+  case class recal (inBam: File, inRecalFile: File, outBam: File, BAD: Boolean) extends TableRecalibration with CommandLineGATKArgs {
+    this.input_file :+= inBam
+    this.recal_file = inRecalFile
+    this.out = outBam
+    this.isIntermediate = false
+    this.analysisName = queueLogDir + outBam + ".recalibration"
+    this.jobName = queueLogDir + outBam + ".recalibration"
+    if (BAD) {
+      this.intervals :+= badInterval
+      this.scatterCount = 85
+    }
+    else
+      this.excludeIntervals :+= badInterval
+  }
+
+  case class analyzeCovariates (inRecalFile: File, outPath: String) extends AnalyzeCovariates {
+    this.jarFile = ACJar
+    this.resources = R
+    this.recal_file = inRecalFile
+    this.output_dir = outPath.toString
+    this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates"
+    this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
+  }
+}
\ No newline at end of file