Commit 38103728 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixing some compile issues

parent 962887bc
...@@ -643,8 +643,6 @@ object VcfStats extends ToolCommand { ...@@ -643,8 +643,6 @@ object VcfStats extends ToolCommand {
val absFile = new File(prefix + ".abs.tsv") val absFile = new File(prefix + ".abs.tsv")
val relFile = new File(prefix + ".rel.tsv") val relFile = new File(prefix + ".rel.tsv")
stats.getContigStats()
absFile.getParentFile.mkdirs() absFile.getParentFile.mkdirs()
val absWriter = new PrintWriter(absFile) val absWriter = new PrintWriter(absFile)
......
...@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.tools.vcfstats ...@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.tools.vcfstats
import java.io.{File, PrintWriter} import java.io.{File, PrintWriter}
import htsjdk.variant.vcf.VCFFileReader import htsjdk.variant.vcf.VCFFileReader
import nl.lumc.sasc.biopet.tools.vcfstats.VcfStats.{cmdArgs, _} import nl.lumc.sasc.biopet.tools.vcfstats.VcfStats._
import nl.lumc.sasc.biopet.utils.{ConfigUtils, FastaUtils, ToolCommand, VcfUtils} import nl.lumc.sasc.biopet.utils.{ConfigUtils, FastaUtils, ToolCommand, VcfUtils}
import nl.lumc.sasc.biopet.utils.intervals.{BedRecord, BedRecordList} import nl.lumc.sasc.biopet.utils.intervals.{BedRecord, BedRecordList}
import org.apache.spark.{SparkConf, SparkContext} import org.apache.spark.{SparkConf, SparkContext}
...@@ -137,7 +137,7 @@ object VcfStatsSpark extends ToolCommand { ...@@ -137,7 +137,7 @@ object VcfStatsSpark extends ToolCommand {
val regionStats = sc.parallelize(regions, regions.size).groupBy(_.chr).map { case (contig, records) => contig -> records.map(readBin(_, samples, cmdArgs, adInfoTags, adGenotypeTags))} val regionStats = sc.parallelize(regions, regions.size).groupBy(_.chr).map { case (contig, records) => contig -> records.map(readBin(_, samples, cmdArgs, adInfoTags, adGenotypeTags))}
val chrStats = regionStats.map {case (contig, stats) => contig -> stats.reduce(_ += _)}.cache() val chrStats = regionStats.map {case (contig, stats) => contig -> stats.reduce(_ += _)}
val totalStats = chrStats.values.reduce(_ += _) val totalStats = chrStats.values.reduce(_ += _)
...@@ -163,8 +163,6 @@ object VcfStatsSpark extends ToolCommand { ...@@ -163,8 +163,6 @@ object VcfStatsSpark extends ToolCommand {
cmdArgs.outputDir + "/sample_compare/allele_overlap", cmdArgs.outputDir + "/sample_compare/allele_overlap",
samples) samples)
Thread.sleep(1000000)
sc.stop sc.stop
logger.info("Done") logger.info("Done")
} }
......
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