From 530a320f2876ff2c3a4e21f3f4ce922963c43fed Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 13 Jul 2010 22:46:08 +0000
Subject: [PATCH] Intermediate commit of scatter/gather recalibation pipeline

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3785 348d0f76-0448-11de-a6fe-93d51630548a
---
 scala/qscript/recalibrate.scala | 60 +++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)
 create mode 100755 scala/qscript/recalibrate.scala

diff --git a/scala/qscript/recalibrate.scala b/scala/qscript/recalibrate.scala
new file mode 100755
index 000000000..c150bc8d7
--- /dev/null
+++ b/scala/qscript/recalibrate.scala
@@ -0,0 +1,60 @@
+import org.broadinstitute.sting.queue.QScript._
+import org.apache.commons.io.FilenameUtils;
+// Other imports can be added here
+
+val unusedArgs = setArgs(args)
+
+def runPipeline() = { 
+    for (bamIn <- inputs(".bam")) {
+      val root = bamIn.getPath()
+      val bamRoot = FilenameUtils.removeExtension(root);
+      val recalData = bamRoot + ".recal_data.csv"
+      val recalBam = bamRoot + ".recal.bam"
+      val recalRecalData = bamRoot + ".recal.recal_data.csv"
+      //add(new CountCovariates(root, recalData, "-OQ"))
+      val tableRecal = new TableRecalibrate(root, recalData, recalBam)
+      tableRecal.intervals = new File("/humgen/gsa-hpprojects/GATK/data/chromosomes.hg18.interval_list")
+      tableRecal.scatterCount = 25
+      add(tableRecal)
+      add(new Index(recalBam))
+      add(new CountCovariates(recalBam, recalRecalData))
+      add(new AnalyzeCovariates(recalData, recalData + ".analyzeCovariates"))
+      add(new AnalyzeCovariates(recalRecalData, recalRecalData + ".analyzeCovariates"))
+    }
+}
+
+runPipeline()
+
+// Populate parameters passed in via -P
+setParams
+
+// Run the pipeline
+run
+
+class Index(bamIn: String) extends GatkFunction {
+    @Input(doc="foo") var bam = bamIn
+    memoryLimit = Some(1)
+    def commandLine = "samtools index %s".format(bam)
+}
+
+class CountCovariates(bamIn: String, recalDataIn: String, args: String = "") extends GatkFunction {
+    @Input(doc="foo") var bam = bamIn
+    @Output(doc="foo") var recalData = recalDataIn
+    memoryLimit = Some(4)
+    def commandLine = gatkCommandLine("CountCovariates") + args + " -l INFO -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -I %s --max_reads_at_locus 20000 -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile %s".format(bam, recalData)
+}
+
+class TableRecalibrate(bamInArg: String, recalDataIn: String, bamOutArg: String) extends GatkFunction {
+    @Input(doc="foo") var bamIn = bamInArg
+    @Input(doc="foo") var recalData = recalDataIn
+    @Gather(classOf[BamGatherFunction])
+    @Output(doc="foo") var bamOut = new File(bamOutArg)
+    memoryLimit = Some(2)
+    def commandLine = gatkCommandLine("TableRecalibration") + "-l INFO -I %s -recalFile %s -outputBam %s".format(bamIn, recalData, bamOut.getPath())
+}
+
+class AnalyzeCovariates(recalDataIn: String, outputDir: String) extends GatkFunction {
+    @Input(doc="foo") var recalData = recalDataIn
+    memoryLimit = Some(4)
+    def commandLine = "java -Xmx4g -jar /home/radon01/depristo/dev/GenomeAnalysisTK/trunk/dist/AnalyzeCovariates.jar -recalFile %s -outputDir %s -resources /home/radon01/depristo/dev/GenomeAnalysisTK/trunk/R/ -ignoreQ 5".format(recalData, outputDir)
+}
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