restore epsilon, add debugging statement

broadinstitute · Dec 11, 2023 · 636d139 · 636d139
1 parent 5576927
commit 636d139
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Showing 3 changed files with 6 additions and 2 deletions.
diff --git a/...titute/hellbender/tools/walkers/vqsr/scalable/ScoreVariantAnnotationsIntegrationTest.java b/...titute/hellbender/tools/walkers/vqsr/scalable/ScoreVariantAnnotationsIntegrationTest.java
@@ -43,7 +43,7 @@ public static void runH5Diff(final String expected, final String actual) {
         // -r: Report mode. Print the differences.
         // --use-system-epsilon: Return a difference if and only if the difference between two data values exceeds
         //                       the system value for epsilon.
-        final String[] command = new String[] { "h5diff", "-r", expected, actual };
+        final String[] command = new String[] { "h5diff", "-r", "--use-system-epsilon", expected, actual };
 
         runProcessAndCaptureOutputInExceptionMessage(controller, command);
     }

diff --git a/...e/hellbender/tools/walkers/vqsr/scalable/TrainVariantAnnotationsModelIntegrationTest.java b/...e/hellbender/tools/walkers/vqsr/scalable/TrainVariantAnnotationsModelIntegrationTest.java
@@ -45,7 +45,7 @@ public static void runH5Diff(final String expected, final String actual) {
         // -r: Report mode. Print the differences.
         // --use-system-epsilon: Return a difference if and only if the difference between two data values exceeds
         //                       the system value for epsilon.
-        final String[] command = new String[] { "h5diff", "-r", expected, actual };
+        final String[] command = new String[] { "h5diff", "-r", "--use-system-epsilon", expected, actual };
 
         runProcessAndCaptureOutputInExceptionMessage(controller, command);
     }

diff --git a/src/testUtils/java/org/broadinstitute/hellbender/testutils/BaseTest.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/BaseTest.java
@@ -111,6 +111,10 @@ public static void runProcess(final ProcessController processController, final S
         final String fullMessage = includeProcessOutputInExceptionMessage ?
                 message + "\n***Process stdout:***\n" + output.getStdout() + "\n***Process stderr:***\n" + output.getStderr() :
                 message;
+
+        // Temporarily print the stdout/stderr unconditionally, for debugging
+        System.err.println(fullMessage);
+
         Assert.assertEquals(output.getExitValue(), 0, fullMessage);
     }