From bffb8bb01f0838cd10e8ff64b83869c9218ab73f Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 8 Oct 2010 14:04:53 +0000
Subject: [PATCH] The SVN repository is not for dumb analysis-specific scripts.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4460 348d0f76-0448-11de-a6fe-93d51630548a
---
 scala/qscript/chartl/omni_bootstrap_refine.q | 124 -------------------
 1 file changed, 124 deletions(-)
 delete mode 100755 scala/qscript/chartl/omni_bootstrap_refine.q

diff --git a/scala/qscript/chartl/omni_bootstrap_refine.q b/scala/qscript/chartl/omni_bootstrap_refine.q
deleted file mode 100755
index e20fcf550..000000000
--- a/scala/qscript/chartl/omni_bootstrap_refine.q
+++ /dev/null
@@ -1,124 +0,0 @@
-import java.io.{FileReader, File, BufferedReader}
-import net.sf.picard.reference.FastaSequenceFile
-import org.broadinstitute.sting.datasources.pipeline.Pipeline
-import org.broadinstitute.sting.gatk.DownsampleType
-import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeCalculationModel.Model
-import org.broadinstitute.sting.queue.extensions.gatk._
-import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
-import org.broadinstitute.sting.queue.extensions.samtools._
-import org.broadinstitute.sting.queue.{QException, QScript}
-import collection.JavaConversions._
-import org.broadinstitute.sting.utils.yaml.YamlUtils
-import org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType
-
-class omni_bootstrap_refine extends QScript {
- => script
-
-  val ref = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
-  val gatkJar = new File("/humgen/gsa-scr1/chartl/sting/dist/GenomeAnalysisTK.jar")
-
-  trait FooTrait extends CommandLineGATK {
-    this.reference_sequence = script.ref
-    this.jarFile = script.gatkJar
-    this.intervalsString :+= "20"
-  }
-
-  class SampleOverlap extends CommandLineFunction {
-    @Input(doc="omni vcf") var omni: File = _
-    @Input(doc="other vcf") var other: File = _
-    @Output(doc="output sn file") var out : File = _
-
-    def commandLine = "%s ; %s ; %s ; %s".format(this.cmd1, this.cmd2, this.cmd3, this.cmd4)
-
-    def cmd1 : String = {
-      return "head -n 500 %s | grep #CHR | cut -f10- | tr '\t' '\n' | sort > temp1".format(omni.getAbsolutePath)
-    }
-
-    def cmd2 : String = {
-      return "head -n 500 %s | grep #CHR | cut -f10- | tr '\t' '\n'| sort > temp2".format(other.getAbsolutePath) 
-    }
-
-    def cmd3 : String = {
-      return "cat temp1 temp2 | sort | uniq -c | awk '{if($1 == 2) print $2}' > %s".format(out.getAbsolutePath)
-    }
-
-    def cmd4 : String = {
-      return "rm temp1 temp2"
-    }
-  }
-
-  class BeagleRefinement extends CommandLineFunction {
-    @Input(doc="The beagle input file") var beagleInput: File = _
-    var beagleOutputBase: String = _
-    var beagleMemoryGigs: Int = 4
-
-    /**
-     * Note: These get set
-     */
-    @Output(doc="The beagle phased file") var beaglePhasedFile: File = _
-    @Output(doc="The beagle likelihood file") var beagleLikelihoods: File = _
-    @Output(doc="The beagle r2 file") var beagleRSquared: File = _
-    var beagleOutputDir: String = _
-
-    def freezeOutputs = {
-      if ( beagleInput.getParent == null ) {
-        beagleOutputDir = ""
-      } else {
-        beagleOutputDir = beagleInput.getParent
-      }
-      beaglePhasedFile = new File(beagleOutputDir+beagleOutputBase+"."+beagleInput.getName+".phased.gz")
-      beagleLikelihoods = new File(beagleOutputDir+beagleOutputBase+"."+beagleInput.getName+".gprobs.gz")
-      beagleRSquared = new File(beagleOutputDir+beagleOutputBase+"."+beagleInput.getName+".r2")
-    }
-
-    def commandLine = "java -Djava.io.tmpdir=%s -Xmx%dg -jar %s like=%s out=%s".format(beagleInput.getParent,beagleMemoryGigs,beagleJar,beagleInput.getAbsolutePath,beagleOutputBase)
-  }
-
-  def runme(pop: File, omni: File, base: String) : List[CommandLineFunction] = {
-    var clf : List[CommandLineFunction] = Nil
-    val s_overlap = new File(base+"_sample_overlap.txt")
-    var calcOverlap = new SampleOverlap
-    calcOverlap.omni = omni
-    calcOverlap.other = pop
-    calcOverlap.out = s_overlap
-
-    clf += calcOverlap
-
-    val subset_omni = swapExt(omni,".vcf","_%s_subset.vcf".format(base))
-    val subset_pop = swapExt(pop,".vcf","_%s_subset.vcf".format(base))
-
-    var omSubset = new SelectVariants with FooTrait
-    omSubset.variantVCF = omni
-    omSubset.sample = s_overlap.getAbsolutePath
-    omSubset.out = subset_omni
-
-    clf += omSubset
-
-    var popSubset = new SelectVariants with FooTrait
-    popSubset.variantVCF = pop
-    popSubset.sample = s_overlap.getAbsolutePath
-    popSubset.out = subset_pop
-
-    clf += popSubset
-
-    var bootRefine = new ProduceBeagleInput with FooTrait
-    bootRefine.variantVCF = popSubset
-    bootRefine.rodBind :+= new RodBind("validation","VCF",subset_omni)
-    bootRefine.bootstrap_vcf = swapExt(subset_omni,".vcf",".boot.vcf")
-    bootRefine.bootstrap = Some(2)
-    bootRefine.validation_genotype_ptrue = Some(0.98);
-    bootRefine.out = new File(base+".beagle_input.beagle")
-
-    clf += bootRefine
-
-    var runBeagle = new BeagleRefinement
-    runBeagle.beagleInput = bootRefine.out
-    runBeagle.beagleOutputBase = base+"_beagle"
-    runBeagle.freezeOutputs()
-
-    clf += runBeagle
-
-    var putBack = new BeagleOutputToVCF with FooTrait
-    putBack.
-  }
-}
\ No newline at end of file