fix failed test

broadinstitute · Mar 21, 2019 · 77b035c · 77b035c
1 parent ef56a86
commit 77b035c
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Showing 3 changed files with 14 additions and 8 deletions.
diff --git a/...n/java/org/broadinstitute/hellbender/tools/walkers/readorientation/CollectF1R2Counts.java b/...n/java/org/broadinstitute/hellbender/tools/walkers/readorientation/CollectF1R2Counts.java
@@ -98,6 +98,7 @@ public List<ReadFilter> getDefaultReadFilters() {
 
     @Override
     public void onTraversalStart() {
+        // TODO: extract a method
         // Initialize for each reference the histogram of the counts of reference sites by depth
         ALL_KMERS.forEach(context -> {
             Histogram<Integer> emptyRefHistogram = F1R2FilterUtils.createRefHistogram(context, maxDepth);

diff --git a/...rg/broadinstitute/hellbender/tools/walkers/readorientation/LearnReadOrientationModel.java b/...rg/broadinstitute/hellbender/tools/walkers/readorientation/LearnReadOrientationModel.java
@@ -76,11 +76,11 @@ public class LearnReadOrientationModel extends CommandLineProgram {
 
     @Override
     protected void onStartup(){
-        Utils.validate(refHistogramFiles.size() == altDataTables.size() && altDataTables.size() == altHistogramFiles.size(),
-                "The numbers of ref histograms, alt histograms, and alt table files must all be the same");
+        Utils.validate(refHistogramFiles.size() == altDataTables.size(), "The same number of ref histograms and alt tables must be provided");
+        Utils.validate(altHistogramFiles.size() == 0 || altDataTables.size() == altHistogramFiles.size(), "If provided, the number of alt histograms must match others");
         refHistograms = sumHistogramsFromFiles(refHistogramFiles, true);
 
-        if (altHistogramFiles != null) {
+        if (altHistogramFiles.size() > 0) {
             altHistograms = sumHistogramsFromFiles(altHistogramFiles, false);
         } else {
             altHistograms = Collections.emptyList();

diff --git a/...ute/hellbender/tools/walkers/readorientation/LearnReadOrientationModelEngineUnitTest.java b/...ute/hellbender/tools/walkers/readorientation/LearnReadOrientationModelEngineUnitTest.java
@@ -26,6 +26,8 @@
 import java.util.*;
 import java.util.stream.IntStream;
 
+import static org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2FilterConstants.ALL_KMERS;
+
 public class LearnReadOrientationModelEngineUnitTest extends CommandLineProgramTest {
     private static final double EPSILON = 1e-3;
 
@@ -224,27 +226,30 @@ public void testReverseComplement() throws IOException {
 
         final List<AltSiteRecord> altDesignMatrix = new ArrayList<>();
 
+        final Map<String, Histogram<Integer>> refSiteHistograms = new HashMap<>(ALL_KMERS.size());
+        ALL_KMERS.forEach(context -> {
+            Histogram<Integer> emptyRefHistogram = F1R2FilterUtils.createRefHistogram(context, F1R2FilterConstants.DEFAULT_MAX_DEPTH);
+            refSiteHistograms.put(context, emptyRefHistogram);
+        });
+
         for (final Triple<String, Nucleotide, ReadOrientation> transition : transitions) {
             final String refContext = transition.getLeft();
             final Nucleotide altAllele = transition.getMiddle();
             final ReadOrientation f1r2 = transition.getRight();
 
-            final Histogram<Integer> refSiteHistogram = F1R2FilterUtils.createRefHistogram(refContext, F1R2FilterConstants.DEFAULT_MAX_DEPTH);
-
-            refSiteHistogram.increment(refDepth, numRefExamples);
-            refMetricsFile.addHistogram(refSiteHistogram);
+            refSiteHistograms.get(refContext).increment(refDepth, numRefExamples);
 
             final int refF1R2 = refDepth / 2;
             final int altF1R2 = f1r2 == ReadOrientation.F1R2 ? altDepth : 0;
 
             IntStream.range(0, numArtifactExamples).forEach(i -> altDesignMatrix.add(new AltSiteRecord(refContext, refDepth, altDepth, refF1R2, altF1R2, altAllele)));
         }
 
+        refSiteHistograms.values().forEach(hist -> refMetricsFile.addHistogram(hist));
         refMetricsFile.write(refHistogramOutput);
         altTableWriter.writeAllRecords(altDesignMatrix);
         altTableWriter.close();
 
-
         final File artifactPriorTable = GATKBaseTest.createTempFile("prior", ".tsv");
         new Main().instanceMain(makeCommandLineArgs(
                 Arrays.asList(