Commit 1efcf0c5 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge stats.json files

parent df582f1a
...@@ -6,7 +6,7 @@ import java.net.URLClassLoader ...@@ -6,7 +6,7 @@ import java.net.URLClassLoader
import htsjdk.variant.variantcontext.{Genotype, VariantContext} import htsjdk.variant.variantcontext.{Genotype, VariantContext}
import htsjdk.variant.vcf.VCFFileReader import htsjdk.variant.vcf.VCFFileReader
import nl.lumc.sasc.biopet.utils.intervals.{BedRecord, BedRecordList} import nl.lumc.sasc.biopet.utils.intervals.{BedRecord, BedRecordList}
import nl.lumc.sasc.biopet.utils.{FastaUtils, ToolCommand, VcfUtils} import nl.lumc.sasc.biopet.utils._
import org.apache.spark.{SparkConf, SparkContext} import org.apache.spark.{SparkConf, SparkContext}
import scala.collection.JavaConversions._ import scala.collection.JavaConversions._
...@@ -108,6 +108,19 @@ object VcfStats extends ToolCommand { ...@@ -108,6 +108,19 @@ object VcfStats extends ToolCommand {
Await.result(totalStats, Duration.Inf) Await.result(totalStats, Duration.Inf)
val completeStatsJson = regions
.flatMap(_.map(_.chr))
.foldLeft(ConfigUtils.fileToConfigMap(new File(cmdArgs.outputDir, "stats.json"))) {
case (map, contig) =>
val contigMap = ConfigUtils.fileToConfigMap(
new File(cmdArgs.outputDir,
"contigs" + File.separator + contig + File.separator + "stats.json"))
ConfigUtils.mergeMaps(map, contigMap)
}
IoUtils.writeLinesToFile(new File(cmdArgs.outputDir, "stats.json"),
ConfigUtils.mapToJson(completeStatsJson).nospaces :: Nil)
sc.stop sc.stop
logger.info("Done") logger.info("Done")
} }
......
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