Simplifies calibration check utility

kevinchern · May 28, 2019 · 0cad03d · 0cad03d
1 parent 9a03b31
commit 0cad03d
Showing 1 changed file with 4 additions and 6 deletions.
diff --git a/src/main/java/humi/v5/CalibrationTest.xtend b/src/main/java/humi/v5/CalibrationTest.xtend
@@ -13,34 +13,32 @@ import org.apache.commons.math3.stat.descriptive.SummaryStatistics
 class CalibrationTest  extends Experiment {
 
   @Arg File reference
-  @Arg String referenceDataset
 
   @Arg File intervals
 
-  @Arg @DefaultValue("dataset")
-  String datasetField = "dataset"
-
   @Arg @DefaultValue("sgrna")
   String sgRNAField = "sgrna"
 
   override run() {
     val truth = loadReference()
     val radia = new SummaryStatistics
     val coverage = new SummaryStatistics
-    for (line : BriefIO::readLines(intervals).indexCSV) { //}.filter[get(datasetField) != referenceDataset]) {
+    for (line : BriefIO::readLines(intervals).indexCSV) { 
       val sgRNA = Integer::parseInt(line.get(sgRNAField))
+      if (!truth.containsKey(sgRNA)) throw new RuntimeException
       val logRatio = Double::parseDouble(line.get(DeltaMethod.Columns.logRatio.toString))
       val radius = Double::parseDouble(line.get(DeltaMethod.Columns.logRatioIntervalRadius.toString))
       radia.addValue(radius)
       coverage.addValue(if (Math::abs(logRatio - truth.get(sgRNA)) < radius) 1.0 else 0.0)
+      truth.remove(sgRNA) 
     }
     println(radia.mean)
     println(coverage.mean)
   }
 
   def loadReference() {
     val result = new LinkedHashMap<Integer, Double>
-    for (line : BriefIO::readLines(reference).indexCSV) { //}.filter[get(datasetField) == referenceDataset]) {
+    for (line : BriefIO::readLines(reference).indexCSV) { 
       val sgRNA = Integer::parseInt(line.get(sgRNAField))
       val logRatio = Double::parseDouble(line.get(DeltaMethod.Columns.logRatio.toString))
       result.put(sgRNA, logRatio)