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Why won't you die? 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5758 348d0f76-0448-11de-a6fe-93d51630548a
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kshakir 2011-05-04 19:13:39 +00:00
parent f7d9f0a1f3
commit 4d251fb91f
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scala/src/org/broadinstitute/sting/queue/util/PipelineUtils.scala
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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
}
}