Changed CNV PoN to filter on equality to interval median percentile.

broadinstitute · Mar 13, 2018 · 73c3f19 · 73c3f19
1 parent 69c0c01
commit 73c3f19
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/...in/java/org/broadinstitute/hellbender/tools/copynumber/CreateReadCountPanelOfNormals.java b/...in/java/org/broadinstitute/hellbender/tools/copynumber/CreateReadCountPanelOfNormals.java
@@ -164,7 +164,7 @@ public final class CreateReadCountPanelOfNormals extends SparkCommandLineProgram
 
     @Argument(
             doc = "Genomic intervals with a median (across samples) of fractional coverage (optionally corrected for GC bias) " +
-                    "below this percentile are filtered out.  " +
+                    "less than or equal to this percentile are filtered out.  " +
                     "(This is the first filter applied.)",
             fullName = MINIMUM_INTERVAL_MEDIAN_PERCENTILE_LONG_NAME,
             minValue = 0.,

diff --git a/...main/java/org/broadinstitute/hellbender/tools/copynumber/denoising/SVDDenoisingUtils.java b/...main/java/org/broadinstitute/hellbender/tools/copynumber/denoising/SVDDenoisingUtils.java
@@ -208,12 +208,12 @@ private static PreprocessedStandardizedResult preprocessPanel(final RealMatrix r
             logger.info(String.format("A value of 0 was provided for argument %s, so the corresponding filtering step will be skipped...",
                     CreateReadCountPanelOfNormals.MINIMUM_INTERVAL_MEDIAN_PERCENTILE_LONG_NAME));
         } else {
-            logger.info(String.format("Filtering intervals with median (across samples) below the %.2f percentile...", minimumIntervalMedianPercentile));
+            logger.info(String.format("Filtering intervals with median (across samples) less than or equal to the %.2f percentile...", minimumIntervalMedianPercentile));
             //calculate percentile
             final double minimumIntervalMedianThreshold = new Percentile(minimumIntervalMedianPercentile).evaluate(originalIntervalMedians);
             //filter intervals
             IntStream.range(0, numOriginalIntervals)
-                    .filter(intervalIndex -> originalIntervalMedians[intervalIndex] < minimumIntervalMedianThreshold)
+                    .filter(intervalIndex -> originalIntervalMedians[intervalIndex] <= minimumIntervalMedianThreshold)
                     .forEach(intervalIndex -> filterIntervals[intervalIndex] = true);
             logger.info(String.format("After filtering, %d out of %d intervals remain...", countNumberPassingFilter(filterIntervals), numOriginalIntervals));
         }