Allowed use of zero eigensamples in DenoiseReadCounts.

src/main/java/org/broadinstitute/hellbender/tools/copynumber/DenoiseReadCounts.java

@@ -166,6 +166,7 @@ public final class DenoiseReadCounts extends CommandLineProgram {
                     "If not specified or if the number of eigensamples available in the panel of normals " +
                     "is smaller than this, all eigensamples will be used.",
             fullName = CopyNumberStandardArgument.NUMBER_OF_EIGENSAMPLES_LONG_NAME,
+            minValue = 0,
             optional = true
     )
     private Integer numEigensamplesRequested = null;
@@ -176,8 +177,6 @@ protected Object doWork() {
             throw new UserException.HardwareFeatureException("Cannot load the required HDF5 library. " +
                     "HDF5 is currently supported on x86-64 architecture and Linux or OSX systems.");
         }
-        Utils.validateArg(numEigensamplesRequested == null || numEigensamplesRequested > 0,
-                "Number of eigensamples to use for denoising must be non-negative.");
 
         IOUtils.canReadFile(inputReadCountFile);
         logger.info(String.format("Reading read-counts file (%s)...", inputReadCountFile));

src/main/java/org/broadinstitute/hellbender/tools/copynumber/denoising/SVDDenoisingUtils.java

@@ -112,7 +112,7 @@ static SVDDenoisedCopyRatioResult denoise(final SVDReadCountPanelOfNormals panel
         if (!CopyNumberArgumentValidationUtils.isSameDictionary(panelOfNormals.getSequenceDictionary(), readCounts.getMetadata().getSequenceDictionary())) {
             logger.warn("Sequence dictionaries in panel and case sample do not match.");
         }
-        ParamUtils.isPositive(numEigensamples, "Number of eigensamples to use for denoising must be positive.");
+        ParamUtils.isPositiveOrZero(numEigensamples, "Number of eigensamples to use for denoising must be non-negative.");
         Utils.validateArg(numEigensamples <= panelOfNormals.getNumEigensamples(),
                 "Number of eigensamples to use for denoising is greater than the number available in the panel of normals.");
 
@@ -424,6 +424,10 @@ public double visit(int sampleIndex, int intervalIndex, double value) {
     private static RealMatrix subtractProjection(final RealMatrix standardizedValues,
                                                  final double[][] eigensampleVectors,
                                                  final int numEigensamples) {
+        if (numEigensamples == 0) {
+            return standardizedValues.copy();
+        }
+
         final int numIntervals = eigensampleVectors.length;
         final int numAllEigensamples = eigensampleVectors[0].length;
 

src/test/java/org/broadinstitute/hellbender/tools/copynumber/DenoiseReadCountsIntegrationTest.java

@@ -26,7 +26,7 @@ public final class DenoiseReadCountsIntegrationTest extends CommandLineProgramTe
     private static final File WGS_ANNOTATED_INTERVALS_FILE = new File(TEST_SUB_DIR, "denoise-read-counts-wgs-annotated-intervals.tsv");
     private static final File WGS_NO_GC_PON_FILE = new File(largeFileTestDir, "cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5");
     private static final File WGS_DO_GC_PON_FILE = new File(largeFileTestDir, "cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5");
-    private static final List<Integer> NUMBER_OF_EIGENVALUES_LIST = Arrays.asList(null, 1, 10);
+    private static final List<Integer> NUMBER_OF_EIGENVALUES_LIST = Arrays.asList(null, 0, 1, 10);
 
     //create all combinations of arguments
     @DataProvider(name = "dataDenoiseReadCounts")
@@ -47,7 +47,7 @@ public Object[][] dataDenoiseReadCounts() {
                         if (numberOfEigenvalues != null) {
                             arguments.addArgument(CopyNumberStandardArgument.NUMBER_OF_EIGENSAMPLES_LONG_NAME, numberOfEigenvalues.toString());
                         }
-                        data.add(Arrays.asList(arguments, ponFile == null));    //set isStandardizedEqualsDenoised = true if no PoN
+                        data.add(Arrays.asList(arguments, ponFile == null || (numberOfEigenvalues != null && numberOfEigenvalues == 0)));    //set isStandardizedEqualsDenoised = true if no PoN or if number of eigenvalues is zero
                     }
                 }
             }