From 4d251fb91f48d18656f4a790452b970d24543d67 Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 4 May 2011 19:13:39 +0000
Subject: [PATCH] Why won't you die?

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5758 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/queue/util/PipelineUtils.scala      | 101 ------------------
 1 file changed, 101 deletions(-)
 delete mode 100755 scala/src/org/broadinstitute/sting/queue/util/PipelineUtils.scala

diff --git a/scala/src/org/broadinstitute/sting/queue/util/PipelineUtils.scala b/scala/src/org/broadinstitute/sting/queue/util/PipelineUtils.scala
deleted file mode 100755
index 22059df99..000000000
--- a/scala/src/org/broadinstitute/sting/queue/util/PipelineUtils.scala
+++ /dev/null
@@ -1,101 +0,0 @@
-package org.broadinstitute.sting.queue.util
-
-import net.sf.picard.reference.ReferenceSequenceFileFactory
-import java.io.File
-import org.broadinstitute.sting.utils.GenomeLocParser
-import collection.JavaConversions._
-import org.broadinstitute.sting.utils.interval.IntervalUtils
-import org.broadinstitute.sting.queue.pipeline.PipelineArgumentCollection
-import org.broadinstitute.sting.utils.yaml.YamlUtils
-import org.broadinstitute.sting.datasources.pipeline.{PipelineSample, PipelineProject, Pipeline}
-import org.broadinstitute.sting.utils.text.XReadLines
-
-class PipelineUtils {
-
-}
-
-object PipelineUtils{
-
-  def smartSplitContigs(reference: File, intervals: File, sets: Int) : List[List[String]] = {
-    var genomeLocParser: GenomeLocParser = new GenomeLocParser(ReferenceSequenceFileFactory.getReferenceSequenceFile(reference))
-    val targets = IntervalUtils.parseIntervalArguments(genomeLocParser,List(intervals.getAbsolutePath), false)
-
-    // Build up a map of contigs with sizes.
-    var contigSizes = Map.empty[String, Long]
-    // todo -- make this look like functional code for Q's sake
-    //targets.foreach( loc => { contigSizes += loc -> { contigSizes.get(loc.getContig) match { case Some(size) => size + loc.size case None => loc.size } } })
-
-    for (loc <- targets) {
-      val contig = loc.getContig
-      val contigSize = loc.size
-      contigSizes += contig -> {
-        contigSizes.get(contig) match {
-          case Some(size) => size + contigSize
-          case None => contigSize
-        }
-      }
-    }
-
-    // Keep a list of pairs of sizes with lists of contigs.
-    var splitContigs = List.empty[(Long, List[String])]
-    for ((contigName, contigSize) <- contigSizes) {
-      if (splitContigs.size < sets) {
-        // If there are fewer than the requested number of sets, just add this contig.
-        splitContigs :+= contigSize -> List(contigName)
-      } else {
-        // If there is already a number of sets
-        // sort the contigs to get the smallest one first.
-        splitContigs = splitContigs.sortBy{case (size, contigs) => size}
-        // Update the pair with the new contig size and name.
-        var smallContigs = splitContigs.head
-        smallContigs = (smallContigs._1 + contigSize) -> (smallContigs._2 :+ contigName)
-        // Re add the pair to the list.
-        splitContigs = smallContigs :: splitContigs.tail
-      }
-    }
-
-    splitContigs.map{case (size, contigs) => contigs}
-  }
-
-  def loadPipelineFromPAC(args: PipelineArgumentCollection) : Pipeline = {
-    if ( args.yamlFile != null ) {
-      return YamlUtils.load(classOf[Pipeline], args.yamlFile)
-    } else {
-      return loadPipelineFromSpec(args.projectName,args.projectRef,args.projectIntervals,args.projectDBSNP,args.projectBams)
-    }
-  }
-
-  def loadPipelineFromSpec(name: String, ref: File, ivals: File, dbsnp: File, pBamList: File) : Pipeline = {
-    var newPipeline : Pipeline = new Pipeline
-    var pipeProject : PipelineProject = new PipelineProject
-    var pipeSamples : List[PipelineSample] = ((new XReadLines(pBamList)).readLines).toList.map( bamSpecToSample )
-
-    pipeProject.setName(name)
-    pipeProject.setReferenceFile(ref)
-    pipeProject.setIntervalList(ivals)
-    pipeProject.setGenotypeDbsnp(dbsnp)
-
-    newPipeline.setProject(pipeProject)
-    newPipeline.setSamples(pipeSamples)
-    
-    return newPipeline
-  }
-
-  //todo -- find a better name for this function
-  def bamSpecToSample(spec: String) : PipelineSample = {
-    var sam : PipelineSample = new PipelineSample
-    var spStr : Array[String] = spec.split("\\s")
-    sam.setId(spStr(0))
-    var tagStr : Array[String] = spStr(1).split(",")
-    var tagMap : java.util.HashMap[String,String] = new java.util.HashMap[String,String](tagStr.size)
-    tagStr.filter( u => ! u.equals("")).foreach( u => tagMap.put(u.split(":")(0),u.split(":")(1)) )
-    sam.setTags(tagMap)
-    var bamStr : Array[String] = spStr(2).split(",")
-    var bamMap : java.util.HashMap[String,File] = new java.util.HashMap[String,File](bamStr.size)
-    bamStr.foreach( u => bamMap.put( u.split(":")(0), new File(u.split(":")(1) ) ) )
-    sam.setBamFiles(bamMap)
-
-    return sam
-
-  }
-}
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