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broadinstitute · Mar 30, 2020 · 6f78819 · 6f78819
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commit 6f78819
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Showing 2 changed files with 22 additions and 7 deletions.
diff --git a/.../hellbender/tools/copynumber/utils/genotyping/NaiveHeterozygousPileupGenotypingUtils.java b/.../hellbender/tools/copynumber/utils/genotyping/NaiveHeterozygousPileupGenotypingUtils.java
@@ -26,17 +26,26 @@ public static class NaiveHeterozygousPileupGenotypingResult {
         private final AllelicCountCollection hetAllelicCounts;
         private final AllelicCountCollection hetNormalAllelicCounts;
 
-
+        /**
+         * @param hetNormalAllelicCounts    {@code null}, if result generated in case-only mode
+         */
         NaiveHeterozygousPileupGenotypingResult(final AllelicCountCollection hetAllelicCounts,
                                                 final AllelicCountCollection hetNormalAllelicCounts) {
             this.hetAllelicCounts = Utils.nonNull(hetAllelicCounts);
             this.hetNormalAllelicCounts = hetNormalAllelicCounts;
+            if (hetNormalAllelicCounts != null) {
+                Utils.validateArg(hetAllelicCounts.getIntervals().equals(hetNormalAllelicCounts.getIntervals()),
+                        "Allelic-count sites in NaiveHeterozygousPileupGenotypingResult must match across case and matched-normal samples.");
+            }
         }
 
         public AllelicCountCollection getHetAllelicCounts() {
             return hetAllelicCounts;
         }
 
+        /**
+         * @return {@code null}, if result generated in case-only mode
+         */
         public AllelicCountCollection getHetNormalAllelicCounts() {
             return hetNormalAllelicCounts;
         }

diff --git a/...est/java/org/broadinstitute/hellbender/tools/copynumber/ModelSegmentsIntegrationTest.java b/...est/java/org/broadinstitute/hellbender/tools/copynumber/ModelSegmentsIntegrationTest.java
@@ -1,6 +1,7 @@
 package org.broadinstitute.hellbender.tools.copynumber;
 
 import org.broadinstitute.hellbender.CommandLineProgramTest;
+import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
 import org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils;
@@ -26,17 +27,21 @@
  */
 public final class ModelSegmentsIntegrationTest extends CommandLineProgramTest {
     private static final File TEST_SUB_DIR = new File(toolsTestDir, "copynumber");
-    private static final File TUMOR_DENOISED_COPY_RATIOS_FILE = new File(TEST_SUB_DIR,
-            "model-segments-wes-tumor-denoised-copy-ratios-SM-74P4M-v1-chr20-downsampled.deduplicated.denoisedCR.tsv");
-    private static final File TUMOR_ALLELIC_COUNTS_FILE = new File(TEST_SUB_DIR,
-            "model-segments-wes-tumor-allelic-counts-SM-74P4M-v1-chr20-downsampled.deduplicated.allelicCounts.tsv");
-    private static final File NORMAL_ALLELIC_COUNTS_FILE = new File(TEST_SUB_DIR,
-            "model-segments-wes-normal-allelic-counts-SM-74NEG-v1-chr20-downsampled.deduplicated.allelicCounts.tsv");
+//    private static final File TUMOR_DENOISED_COPY_RATIOS_FILE = new File(TEST_SUB_DIR,
+//            "model-segments-wes-tumor-denoised-copy-ratios-SM-74P4M-v1-chr20-downsampled.deduplicated.denoisedCR.tsv");
+//    private static final File TUMOR_ALLELIC_COUNTS_FILE = new File(TEST_SUB_DIR,
+//            "model-segments-wes-tumor-allelic-counts-SM-74P4M-v1-chr20-downsampled.deduplicated.allelicCounts.tsv");
+//    private static final File NORMAL_ALLELIC_COUNTS_FILE = new File(TEST_SUB_DIR,
+//            "model-segments-wes-normal-allelic-counts-SM-74NEG-v1-chr20-downsampled.deduplicated.allelicCounts.tsv");
     private static final File TUMOR_DENOISED_COPY_RATIOS_WITH_SAMPLE_NAME_MISMATCH_FILE = new File(TEST_SUB_DIR,
             "model-segments-wes-tumor-denoised-copy-ratios-with-sample-name-mismatch.denoisedCR.tsv");
     private static final File NORMAL_ALLELIC_COUNTS_FILE_WITH_MISSING_SITES = new File(TEST_SUB_DIR,
             "model-segments-wes-normal-allelic-counts-with-missing-sites.allelicCounts.tsv");
 
+    private static final File TUMOR_DENOISED_COPY_RATIOS_FILE = new File("/home/slee/working/germline-tagging/REBC-AC9B/chr13.REBC-AC9B-TTP1-A-1-1-D-A525-36.denoisedCR.tsv");
+    private static final File TUMOR_ALLELIC_COUNTS_FILE = new File("/home/slee/working/germline-tagging/REBC-AC9B/chr13.REBC-AC9B-TTP1-A-1-1-D-A525-36.allelicCounts.tsv");
+    private static final File NORMAL_ALLELIC_COUNTS_FILE = new File("/home/slee/working/germline-tagging/REBC-AC9B/chr13.REBC-AC9B-NB1-A-1-0-D-A553-36.allelicCounts.tsv");
+
     private static final SampleLocatableMetadata EXPECTED_METADATA = new CopyRatioCollection(TUMOR_DENOISED_COPY_RATIOS_FILE).getMetadata();
 
     @Test
@@ -48,6 +53,7 @@ public void testAllInputsAvailable() {
                 .add(CopyNumberStandardArgument.ALLELIC_COUNTS_FILE_LONG_NAME, TUMOR_ALLELIC_COUNTS_FILE.getAbsolutePath())
                 .add(CopyNumberStandardArgument.NORMAL_ALLELIC_COUNTS_FILE_LONG_NAME, NORMAL_ALLELIC_COUNTS_FILE.getAbsolutePath())
                 .addOutput(outputDir)
+                .add(StandardArgumentDefinitions.VERBOSITY_NAME, "INFO")
                 .add(CopyNumberStandardArgument.OUTPUT_PREFIX_LONG_NAME, outputPrefix);
         runCommandLine(argsBuilder);
         assertOutputFiles(outputDir, outputPrefix, true, true);