Added check to skip outlier truncation if number of matrix elements e…

…xceeds Integer.MAX_VALUE in CreateReadCountPanelOfNormals. (#4734)
broadinstitute · Mar 2, 2019 · e363ff9 · e363ff9
1 parent 994e987
commit e363ff9
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/...main/java/org/broadinstitute/hellbender/tools/copynumber/denoising/SVDDenoisingUtils.java b/...main/java/org/broadinstitute/hellbender/tools/copynumber/denoising/SVDDenoisingUtils.java
@@ -332,6 +332,8 @@ public double visit(int sampleIndex, int intervalIndex, double value) {
         if (extremeOutlierTruncationPercentile == 0.) {
             logger.info(String.format("A value of 0 was provided for argument %s, so the corresponding truncation step will be skipped...",
                     CreateReadCountPanelOfNormals.EXTREME_OUTLIER_TRUNCATION_PERCENTILE_LONG_NAME));
+        } else if ((long) preprocessedReadCounts.getRowDimension() * preprocessedReadCounts.getColumnDimension() > Integer.MAX_VALUE) {
+            logger.warn("The number of matrix elements exceeds Integer.MAX_VALUE, so outlier truncation will be skipped...");
         } else {
             final double[] values = Doubles.concat(preprocessedReadCounts.getData());
             final double minimumOutlierTruncationThreshold = new Percentile(extremeOutlierTruncationPercentile).evaluate(values);