Merge pull request #171 from biopet/fix-BIOPET-759

Merge stats.json files

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

@@ -165,7 +165,7 @@ case class Stats(generalStats: mutable.Map[String, mutable.Map[Any, Int]] = muta
                      sampleDistributions: List[String],
                      contig: Option[String]): Unit = {
     outputDir.mkdirs()
-    this.writeToFile(new File(outputDir, "stats.json"),
+    this.writeToFile(new File(outputDir, s"${contig.getOrElse("total")}.json"),
                      samples,
                      genotypeFields,
                      infoFields,

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

@@ -6,7 +6,7 @@ import java.net.URLClassLoader
 import htsjdk.variant.variantcontext.{Genotype, VariantContext}
 import htsjdk.variant.vcf.VCFFileReader
 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 scala.collection.JavaConversions._
@@ -108,6 +108,19 @@ object VcfStats extends ToolCommand {
 
     Await.result(totalStats, Duration.Inf)
 
+    val completeStatsJson = regions
+      .flatMap(_.map(_.chr))
+      .foldLeft(ConfigUtils.fileToConfigMap(new File(cmdArgs.outputDir, "total.json"))) {
+        case (map, contig) =>
+          val contigMap = ConfigUtils.fileToConfigMap(
+            new File(cmdArgs.outputDir,
+                     "contigs" + File.separator + contig + File.separator + s"$contig.json"))
+          ConfigUtils.mergeMaps(map, contigMap)
+      }
+
+    IoUtils.writeLinesToFile(new File(cmdArgs.outputDir, "stats.json"),
+                             ConfigUtils.mapToJson(completeStatsJson).nospaces :: Nil)
+
     sc.stop
     logger.info("Done")
   }

biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala

@@ -284,44 +284,6 @@ class VcfStatsTest extends TestNGSuite with Matchers {
     general.get("NotFiltered") shouldEqual Some(1)
     general.get("Symbolic") shouldEqual Some(0)
     general.get("SimpleInsertion") shouldEqual Some(1)
-
-    val total = generalStats
-    total.get("SampleDistribution-NonInformative") shouldEqual Some(Map(0 -> 1))
-    total.get("SampleDistribution-Called") shouldEqual Some(Map(3 -> 1))
-    total.get("SampleDistribution-Mixed") shouldEqual Some(Map(0 -> 1))
-    total.get("SampleDistribution-Hom") shouldEqual Some(Map(1 -> 1))
-    total.get("SampleDistribution-HomRef") shouldEqual Some(Map(1 -> 1))
-    total.get("SampleDistribution-Available") shouldEqual Some(Map(3 -> 1))
-    total.get("QUAL") shouldEqual Some(Map(1541 -> 1))
-    total.get("SampleDistribution-HetNonRef") shouldEqual Some(Map(0 -> 1))
-    total.get("SampleDistribution-Het") shouldEqual Some(Map(2 -> 1))
-    total.get("SampleDistribution-NoCall") shouldEqual Some(Map(0 -> 1))
-    total.get("SampleDistribution-Filtered") shouldEqual Some(Map(0 -> 1))
-    total.get("SampleDistribution-HomVar") shouldEqual Some(Map(0 -> 1))
-    total.get("SampleDistribution-Variant") shouldEqual Some(Map(2 -> 1))
-
-    generalStats.get("general") should not be empty
-    val totGeneral = generalStats("general")
-
-    totGeneral.get("PolymorphicInSamples") shouldEqual Some(1)
-    totGeneral.get("ComplexIndel") shouldEqual Some(0)
-    totGeneral.get("FullyDecoded") shouldEqual Some(0)
-    totGeneral.get("PointEvent") shouldEqual Some(0)
-    totGeneral.get("MNP") shouldEqual Some(0)
-    totGeneral.get("Indel") shouldEqual Some(1)
-    totGeneral.get("Biallelic") shouldEqual Some(1)
-    totGeneral.get("SimpleDeletion") shouldEqual Some(0)
-    totGeneral.get("Variant") shouldEqual Some(1)
-    totGeneral.get("SymbolicOrSV") shouldEqual Some(0)
-    totGeneral.get("MonomorphicInSamples") shouldEqual Some(0)
-    totGeneral.get("SNP") shouldEqual Some(0)
-    totGeneral.get("Filtered") shouldEqual Some(0)
-    totGeneral.get("StructuralIndel") shouldEqual Some(0)
-    totGeneral.get("Total") shouldEqual Some(1)
-    totGeneral.get("Mixed") shouldEqual Some(0)
-    totGeneral.get("NotFiltered") shouldEqual Some(1)
-    totGeneral.get("Symbolic") shouldEqual Some(0)
-    totGeneral.get("SimpleInsertion") shouldEqual Some(1)
   }
 
   @Test
@@ -354,29 +316,5 @@ class VcfStatsTest extends TestNGSuite with Matchers {
     general.get("Available") shouldEqual Some(1)
     general.get("Het") shouldEqual Some(1)
     general.get("HetNonRef") shouldEqual Some(0)
-
-    val total = genotypeStats
-    total.get("GQ") shouldEqual Some(Map(99 -> 1))
-    total.get("AD") shouldEqual Some(Map(24 -> 1, 21 -> 1))
-    total.get("AD-used") shouldEqual Some(Map(24 -> 1, 21 -> 1))
-    total.get("DP") shouldEqual Some(Map(45 -> 1))
-    total.get("AD-alt") shouldEqual Some(Map(21 -> 1))
-    total.get("AD-ref") shouldEqual Some(Map(24 -> 1))
-    total.get("general") should not be empty
-
-    val totGeneral = genotypeStats("general")
-    totGeneral.get("Hom") shouldEqual Some(0)
-    totGeneral.get("NoCall") shouldEqual Some(0)
-    totGeneral.get("Variant") shouldEqual Some(1)
-    totGeneral.get("Filtered") shouldEqual Some(0)
-    totGeneral.get("NonInformative") shouldEqual Some(0)
-    totGeneral.get("Called") shouldEqual Some(1)
-    totGeneral.get("Total") shouldEqual Some(1)
-    totGeneral.get("HomVar") shouldEqual Some(0)
-    totGeneral.get("HomRef") shouldEqual Some(0)
-    totGeneral.get("Mixed") shouldEqual Some(0)
-    totGeneral.get("Available") shouldEqual Some(1)
-    totGeneral.get("Het") shouldEqual Some(1)
-    totGeneral.get("HetNonRef") shouldEqual Some(0)
   }
 }