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Update VEP.scala #4

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Update VEP.scala #4

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34 changes: 28 additions & 6 deletions src/main/scala/extprg/vep/VEP.scala
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Original file line number Diff line number Diff line change
@@ -1,7 +1,16 @@

package extprg.vep

import org.apache.spark.SparkContext
import org.apache.spark.storage.StorageLevel
import org.apache.spark.rdd.RDD
import org.apache.hadoop.fs.{FileSystem, Path}
import org.apache.hadoop.conf.Configuration
import org.apache.hadoop.io.IOUtils
import org.apache.hadoop.io.compress.CompressionCodec
import scala.reflect.io.Directory
import java.io.File
import java.io._
import utils.CustomOperators.RDDOperators

object VEP {
Expand All @@ -15,14 +24,27 @@ object VEP {
val dataRDD = sc.textFile(inputPath)
val (headerRDD, variantsRDD) = dataRDD.filterDivisor(line => line.startsWith("#"))
val gatheredHeaderRDD = headerRDD.coalesce(1)
val outputHeaderRDD = gatheredHeaderRDD.pipe(annotateCmd)
val numberOfLines: Long = variantsRDD.persist(StorageLevel.MEMORY_AND_DISK).count()
val vepBufferSize: Long = 29000
val vepBufferSize: Long = 20000
val numberOfPartitions = numberOfLines/vepBufferSize
variantsRDD.repartition(numberOfPartitions.toInt)
val outputVariantsRDD = variantsRDD.pipe(annotateCmd).filter(line => !line.startsWith("#"))
outputHeaderRDD
//val numberOfPartitions = 50

val directory = new Directory(new File(s"/vagrant/tmp/*"))
directory.deleteRecursively()


val tmp = variantsRDD.collect().toList.sliding(vepBufferSize.toInt, vepBufferSize.toInt).toList
tmp.zipWithIndex.foreach{case (line,i) => val pw = new PrintWriter(new File(s"/vagrant/tmp/tmp_$i.vcf")); pw.write(headerRDD.union(sc.makeRDD(line)).collect().toList.mkString("\n")); pw.close}
//tmp.zipWithIndex.foreach{case (line,i) => gatheredHeaderRDD.union(sc.makeRDD(line)).coalesce(1).saveAsTextFile(s"file:///vagrant/tmp/tmp_$i/")}
//val eachFile = tmp.map(line => gatheredHeaderRDD.union(sc.makeRDD(line)))
//val kk = sc.makeRDD(tmp)
val p = sc.makeRDD(List.range(0, tmp.size).map(line => s"/vagrant/tmp/tmp_$line.vcf")).repartition(numberOfPartitions.toInt)
val outputVariantsRDD = p.pipe(annotateCmd).filter(line => !line.startsWith("#"))
gatheredHeaderRDD
.union(outputVariantsRDD)
.saveAsSingleTextFile(outputPath)
}
}
}


}