Remove old version and replace by the spark version

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStatsArgs.scala

@@ -2,12 +2,7 @@ package nl.lumc.sasc.biopet.tools.vcfstats
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.tools.vcfstats.VcfStats.{
-  defaultGenotypeFields,
-  defaultInfoFields,
-  generalWiggleOptions,
-  genotypeWiggleOptions
-}
+import nl.lumc.sasc.biopet.tools.vcfstats.VcfStats.{defaultGenotypeFields, defaultInfoFields}
 import nl.lumc.sasc.biopet.utils.AbstractOptParser
 
 /**
@@ -26,8 +21,6 @@ case class VcfStatsArgs(inputFile: File = null,
                         binSize: Int = 10000000,
                         maxContigsInSingleJob: Int = 250,
                         writeBinStats: Boolean = false,
-                        generalWiggle: List[String] = Nil,
-                        genotypeWiggle: List[String] = Nil,
                         localThreads: Int = 1,
                         sparkMaster: Option[String] = None,
                         contigSampleOverlapPlots: Boolean = false)
@@ -80,18 +73,6 @@ class VcfStatsOptParser(cmdName: String) extends AbstractOptParser[VcfStatsArgs]
   opt[Unit]("writeBinStats") unbounded () action { (_, c) =>
     c.copy(writeBinStats = true)
   } text "Write bin statistics. Default False"
-  opt[String]("generalWiggle") unbounded () action { (x, c) =>
-    c.copy(generalWiggle = x :: c.generalWiggle, writeBinStats = true)
-  } validate { x =>
-    if (generalWiggleOptions.contains(x)) success else failure(s"""Nonexistent field $x""")
-  } text s"""Create a wiggle track with bin size <binSize> for any of the following statistics:
-            |${generalWiggleOptions.mkString(", ")}""".stripMargin
-  opt[String]("genotypeWiggle") unbounded () action { (x, c) =>
-    c.copy(genotypeWiggle = x :: c.genotypeWiggle, writeBinStats = true)
-  } validate { x =>
-    if (genotypeWiggleOptions.contains(x)) success else failure(s"""Non-existent field $x""")
-  } text s"""Create a wiggle track with bin size <binSize> for any of the following genotype fields:
-            |${genotypeWiggleOptions.mkString(", ")}""".stripMargin
   opt[Int]('t', "localThreads") unbounded () action { (x, c) =>
     c.copy(localThreads = x)
   } text s"Number of local threads to use"

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStatsSpark.scala

-package nl.lumc.sasc.biopet.tools.vcfstats
-
-import java.io.{File, PrintWriter}
-import java.net.URLClassLoader
-
-import htsjdk.variant.vcf.VCFFileReader
-import nl.lumc.sasc.biopet.tools.vcfstats.VcfStats._
-import nl.lumc.sasc.biopet.utils.intervals.{BedRecord, BedRecordList}
-import nl.lumc.sasc.biopet.utils.{ConfigUtils, ToolCommand, VcfUtils}
-import org.apache.spark.{SparkConf, SparkContext}
-
-import scala.collection.JavaConversions._
-
-/**
-  * Created by pjvanthof on 14/07/2017.
-  */
-object VcfStatsSpark extends ToolCommand {
-
-  type Args = VcfStatsArgs
-
-  def main(args: Array[String]): Unit = {
-
-    logger.info("Started")
-    val argsParser = new VcfStatsOptParser(commandName)
-    val cmdArgs = argsParser.parse(args, VcfStatsArgs()) getOrElse (throw new IllegalArgumentException)
-
-    val reader = new VCFFileReader(cmdArgs.inputFile, true)
-    val header = reader.getFileHeader
-    val samples = header.getSampleNamesInOrder.toList
-
-    reader.close()
-
-    val adInfoTags = {
-      (for (infoTag <- cmdArgs.infoTags if !defaultInfoFields.contains(infoTag)) yield {
-        require(header.getInfoHeaderLine(infoTag) != null,
-                "Info tag '" + infoTag + "' not found in header of vcf file")
-        infoTag
-      }) ::: (for (line <- header.getInfoHeaderLines if cmdArgs.allInfoTags
-                   if !defaultInfoFields.contains(line.getID)
-                   if !cmdArgs.infoTags.contains(line.getID)) yield {
-        line.getID
-      }).toList ::: defaultInfoFields
-    }
-
-    val adGenotypeTags = (for (genotypeTag <- cmdArgs.genotypeTags
-                               if !defaultGenotypeFields.contains(genotypeTag)) yield {
-      require(header.getFormatHeaderLine(genotypeTag) != null,
-              "Format tag '" + genotypeTag + "' not found in header of vcf file")
-      genotypeTag
-    }) ::: (for (line <- header.getFormatHeaderLines if cmdArgs.allGenotypeTags
-                 if !defaultGenotypeFields.contains(line.getID)
-                 if !cmdArgs.genotypeTags.contains(line.getID)
-                 if line.getID != "PL") yield {
-      line.getID
-    }).toList ::: defaultGenotypeFields
-
-    logger.info("Init spark context")
-
-    val jars = ClassLoader.getSystemClassLoader
-      .asInstanceOf[URLClassLoader]
-      .getURLs
-      .map(_.getFile)
-    val conf = new SparkConf()
-      .setAppName(commandName)
-      .setMaster(cmdArgs.sparkMaster.getOrElse(s"local[${cmdArgs.localThreads}]"))
-      .setJars(jars)
-    val sc = new SparkContext(conf)
-    logger.info("Spark context is up")
-
-    val regions = (cmdArgs.intervals match {
-      case Some(i) =>
-        BedRecordList.fromFile(i).validateContigs(cmdArgs.referenceFile)
-      case _ => BedRecordList.fromReference(cmdArgs.referenceFile)
-    }).combineOverlap
-      .scatter(cmdArgs.binSize, maxContigsInSingleJob = Some(cmdArgs.maxContigsInSingleJob))
-    val contigs = regions.flatMap(_.map(_.chr)).distinct
-
-    val regionStats = sc
-      .parallelize(regions, regions.size)
-      .map(readBin(_, samples, cmdArgs, adInfoTags, adGenotypeTags))
-
-    val totalStats = regionStats.reduce(_ += _)
-
-    val allWriter = new PrintWriter(new File(cmdArgs.outputDir, "stats.json"))
-    val json = ConfigUtils.mapToJson(
-      totalStats.getAllStats(contigs, samples, adGenotypeTags, adInfoTags, sampleDistributions))
-    allWriter.println(json.nospaces)
-    allWriter.close()
-
-    //TODO: write wig files
-
-    writeOverlap(totalStats,
-                 _.genotypeOverlap,
-                 cmdArgs.outputDir + "/sample_compare/genotype_overlap",
-                 samples)
-    writeOverlap(totalStats,
-                 _.alleleOverlap,
-                 cmdArgs.outputDir + "/sample_compare/allele_overlap",
-                 samples)
-
-    sc.stop
-    logger.info("Done")
-  }
-
-  def readBin(bedRecords: List[BedRecord],
-              samples: List[String],
-              cmdArgs: Args,
-              adInfoTags: List[String],
-              adGenotypeTags: List[String]): Stats = {
-    val reader = new VCFFileReader(cmdArgs.inputFile, true)
-    var chunkCounter = 0
-    val stats = Stats.emptyStats(samples)
-
-    for (bedRecord <- bedRecords) {
-      logger.info("Starting on: " + bedRecord)
-
-      val samInterval = bedRecord.toSamInterval
-
-      val query =
-        reader.query(samInterval.getContig, samInterval.getStart, samInterval.getEnd)
-      if (!query.hasNext) {
-        Stats.mergeNestedStatsMap(stats.generalStats, fillGeneral(adInfoTags))
-        for (sample <- samples) yield {
-          Stats.mergeNestedStatsMap(stats.samplesStats(sample).genotypeStats,
-                                    fillGenotype(adGenotypeTags))
-        }
-        chunkCounter += 1
-      }
-
-      for (record <- query if record.getStart <= samInterval.getEnd) {
-        Stats.mergeNestedStatsMap(stats.generalStats, checkGeneral(record, adInfoTags))
-        for (sample1 <- samples) yield {
-          val genotype = record.getGenotype(sample1)
-          Stats.mergeNestedStatsMap(stats.samplesStats(sample1).genotypeStats,
-                                    checkGenotype(record, genotype, adGenotypeTags))
-          for (sample2 <- samples) {
-            val genotype2 = record.getGenotype(sample2)
-            if (genotype.getAlleles == genotype2.getAlleles)
-              stats.samplesStats(sample1).sampleToSample(sample2).genotypeOverlap += 1
-            stats.samplesStats(sample1).sampleToSample(sample2).alleleOverlap += VcfUtils
-              .alleleOverlap(genotype.getAlleles.toList, genotype2.getAlleles.toList)
-          }
-        }
-        chunkCounter += 1
-      }
-    }
-    reader.close()
-
-    stats
-  }
-}