now only accepts intervals files if the user specifically requests to report bams at interval only.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5291 348d0f76-0448-11de-a6fe-93d51630548a

scala/qscript/oneoffs/carneiro/dataProcessing.scala

@@ -25,13 +25,13 @@ class dataProcessing extends QScript {
   var input: String = _
 
   @Input(doc="Reference fasta file", shortName="R", required=false)
-  var reference: File = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
+  var reference: File = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19")
 
   @Input(doc="dbsnp ROD to use (VCF)", shortName="D", required=false)     // todo -- accept any format. Not only VCF.
   val dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
 
   @Input(doc="extra VCF files to use as reference indels for Indel Realignment", shortName="indels", required=false)  //todo -- once vcfs are merged, this will become the only indel vcf to be used and the merged file will be the default.
-  val indels: File = _
+  val indels: File = null
 
   @Input(doc="the project name determines the final output (BAM file) base name. Example NA12878 yields NA12878.processed.bam", shortName="p", required=false)
   var projectName: String = "combined"
@@ -39,12 +39,11 @@ class dataProcessing extends QScript {
   @Input(doc="output path", shortName="outputDir", required=false)
   var outputDir: String = ""
 
-  @Input(doc="the -L interval string to be used by GATK", shortName="L", required=false)
+  @Input(doc="the -L interval string to be used by GATK - output bams at interval only", shortName="L", required=false)
   var intervalString: String = ""
 
-  // todo -- this shouldn't be allowed.  We want a flag that says "output bams at intervals only" or not
+  @Input(doc="output bams at intervals only", shortName="intervals", required=false)
-  @Input(doc="provide a .intervals file with the list of target intervals", shortName="intervals", required=false)
+  var intervals: File = _
-  var intervals: File = new File("/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals")
 
 
   // todo -- let's create a pre-merged single VCF and put it into /humgen/gsa-hpprojects/GATK/data please
@@ -71,6 +70,22 @@ class dataProcessing extends QScript {
     var perLaneBamList: List[String] = Nil
     var recalibratedBamList: List[File] = Nil
 
+
+    // Helpful variables
+    val outName: String        = qscript.projectName
+    val outDir: String         = qscript.outputDir
+
+    // BAM files generated by the pipeline
+    val bamList: String         = outDir + outName + ".list"
+    val cleanedBam: String      = outDir + outName + ".clean.bam"
+    val fixedBam: String        = outDir + outName + ".processed.bam"
+
+    // Accessory files
+    val knownTargetIntervals: String = outDir + outName + ".known_indels.intervals"
+    val allTargetIntervals: String    = outDir + outName + ".all_indels.intervals"
+
+    add(new knownTargets(knownTargetIntervals))
+
     // Populates the list of per lane bam files to process (single bam or list of bams).
     if (input.endsWith("bam"))
       perLaneBamList :+= input
@@ -78,9 +93,6 @@ class dataProcessing extends QScript {
       for (bam <- Source.fromFile(input).getLines())
         perLaneBamList :+= bam
 
-
-
-
     perLaneBamList.foreach { perLaneBam =>
 
       // Helpful variables
@@ -93,15 +105,13 @@ class dataProcessing extends QScript {
       val recalBam: String        = baseName + ".clean.dedup.recal.bam"
 
       // Accessory files
-      val targetIntervals: String = baseName + ".indel.intervals"
       val metricsFile: String     = baseName + ".metrics"
       val preRecalFile: String    = baseName + ".pre_recal.csv"
       val postRecalFile: String   = baseName + ".post_recal.csv"
       val preOutPath: String      = baseName + ".pre"
       val postOutPath: String     = baseName + ".post"
 
-      add(new target(perLaneBam, targetIntervals),
+      add(new clean(perLaneBam, knownTargetIntervals, cleanedBam, knownsOnly, intermediate),
-          new clean(perLaneBam, targetIntervals, cleanedBam, knownsOnly, intermediate),
           new dedup(cleanedBam, dedupedBam, metricsFile),
           new cov(dedupedBam, preRecalFile),
           new recal(dedupedBam, preRecalFile, recalBam),
@@ -112,24 +122,23 @@ class dataProcessing extends QScript {
       recalibratedBamList :+= new File(recalBam)
     }
 
-    // Helpful variables
-    val outName: String        = qscript.projectName
-    val outDir: String         = qscript.outputDir
-
-    // BAM files generated by the pipeline
-    val bamList: String         = outDir + outName + ".list"
-    val cleanedBam: String      = outDir + outName + ".clean.bam"
-    val fixedBam: String        = outDir + outName + ".processed.bam"
-
-    // Accessory files
-    val targetIntervals: String = outDir + outName + ".indel.intervals"
 
     add(new writeList(recalibratedBamList, bamList),
-        new target(bamList, targetIntervals),       // todo -- reuse previously generated intervals (see how to do that)
+        new allTargets(bamList, allTargetIntervals),
-        new clean(bamList, targetIntervals, cleanedBam, !knownsOnly, !intermediate))
+        new clean(bamList, allTargetIntervals, cleanedBam, !knownsOnly, !intermediate))
   }
 
-  class target (inBams: String, outIntervals: String) extends RealignerTargetCreator with CommandLineGATKArgs {
+  class knownTargets (outIntervals: String) extends RealignerTargetCreator with CommandLineGATKArgs {
+      this.out = new File(outIntervals)
+      this.mismatchFraction = Some(0.0)
+      this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
+      this.rodBind :+= RodBind("indels1", "VCF", dindelPilotCalls)
+      this.rodBind :+= RodBind("indels2", "VCF", dindelAFRCalls)
+      this.rodBind :+= RodBind("indels3", "VCF", dindelEURCalls)
+      this.rodBind :+= RodBind("indels4", "VCF", dindelASNCalls)
+  }
+
+  class allTargets (inBams: String, outIntervals: String) extends knownTargets(outIntervals) {
       this.input_file :+= new File(inBams)
       this.out = new File(outIntervals)
       this.mismatchFraction = Some(0.0)
@@ -139,17 +148,13 @@ class dataProcessing extends QScript {
       this.rodBind :+= RodBind("indels3", "VCF", dindelEURCalls)
       this.rodBind :+= RodBind("indels4", "VCF", dindelASNCalls)
       if (qscript.indels != null) this.rodBind :+= RodBind("indels5", "VCF", qscript.indels)
-      this.jobName = inBams + ".tgt"
+      this.jobName = outIntervals + ".target"
-      if (!qscript.intervalString.isEmpty()) this.intervalsString :+= qscript.intervalString
-      else this.intervals :+= qscript.intervals
   }
 
   class clean (inBams: String, tIntervals: String, outBam: String, knownsOnly: Boolean, intermediate: Boolean) extends IndelRealigner with CommandLineGATKArgs {
     this.input_file :+= new File(inBams)
     this.targetIntervals = new File(tIntervals)
     this.out = new File(outBam)
-    this.doNotUseSW = true
-    this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY)
     this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
     this.rodBind :+= RodBind("indels1", "VCF", dindelPilotCalls)
     this.rodBind :+= RodBind("indels2", "VCF", dindelAFRCalls)
@@ -159,27 +164,20 @@ class dataProcessing extends QScript {
     this.useOnlyKnownIndels = knownsOnly
     this.sortInCoordinateOrderEvenThoughItIsHighlyUnsafe = true
     this.constrainMovement = true
+    this.doNotUseSW = true
+    this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY)
+    this.compress = Some(0)
     this.isIntermediate = intermediate
-    this.jobName = inBams + ".clean"
+    this.jobName = outBam + ".clean"
-    if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
+    if (!intermediate && !qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
-    else this.intervals :+= qscript.intervals
+    if (!intermediate && qscript.intervals != null) this.intervals :+= qscript.intervals
-  }
-
-  class fixMates (inBam: String, outBam: String, intermediate: Boolean) extends PicardBamJarFunction {
-    @Input(doc="cleaned bam") var cleaned: File = new File(inBam)
-    @Output(doc="fixed bam") var fixed: File = new File(outBam)
-    override def inputBams = List(cleaned)
-    override def outputBam = fixed
-    override def commandLine = super.commandLine + " CREATE_INDEX=true"
-    this.jarFile = qscript.fixMatesJar
-    this.isIntermediate = intermediate
-    this.memoryLimit = Some(6)
-    this.jobName = inBam + ".fix"
   }
 
   class dedup (inBam: String, outBam: String, metricsFile: String) extends PicardBamJarFunction {
     @Input(doc="fixed bam") var clean: File = new File(inBam)
     @Output(doc="deduped bam") var deduped: File = new File(outBam)
+    @Output(doc="deduped bam index") var dedupedIndex: File = new File(outBam + ".bai")
+    @Output(doc="metrics file") var metrics: File = new File(metricsFile)
     override def inputBams = List(clean)
     override def outputBam = deduped
     override def commandLine = super.commandLine + " M=" + metricsFile + " CREATE_INDEX=true"
@@ -187,7 +185,7 @@ class dataProcessing extends QScript {
     this.memoryLimit = Some(6)
     this.jarFile = qscript.dedupJar
     this.isIntermediate = true
-    this.jobName = inBam + ".dedup"
+    this.jobName = outBam + ".dedup"
   }
 
   class cov (inBam: String, outRecalFile: String) extends CountCovariates with CommandLineGATKArgs {
@@ -195,13 +193,16 @@ class dataProcessing extends QScript {
     this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
     this.input_file :+= new File(inBam)
     this.recal_file = new File(outRecalFile)
+    this.jobName = outRecalFile + ".covariates"
   }
 
   class recal (inBam: String, inRecalFile: String, outBam: String) extends TableRecalibration with CommandLineGATKArgs {
+    @Output(doc="recalibrated bam index") var recalIndex: File = new File(outBam + ".bai")
     this.input_file :+= new File (inBam)
     this.recal_file = new File(inRecalFile)
     this.out = new File(outBam)
     this.index_output_bam_on_the_fly = Some(true)
+    this.jobName = outBam + ".recalibration"
   }
 
   class analyzeCovariates (inRecalFile: String, outPath: String) extends AnalyzeCovariates {
@@ -209,11 +210,12 @@ class dataProcessing extends QScript {
     this.resources = qscript.R
     this.recal_file = new File(inRecalFile)
     this.output_dir = outPath
+    this.jobName = inRecalFile + ".analyze_covariates"
   }
 
   class writeList(inBams: List[File], outBamList: String) extends ListWriterFunction {
     this.inputFiles = inBams
     this.listFile = new File(outBamList)
-    this.jobName = "bamList"
+    this.jobName = outBamList + ".bamList"
   }
 }