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broadinstitute · Feb 11, 2025 · 0b38737 · 0b38737
1 parent d54015b
commit 0b38737
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Showing 3 changed files with 8 additions and 6 deletions.
diff --git a/src/main/java/picard/fingerprint/ExtractFingerprint.java b/src/main/java/picard/fingerprint/ExtractFingerprint.java
@@ -26,6 +26,7 @@
 
 import htsjdk.samtools.util.IOUtil;
 import htsjdk.samtools.util.Log;
+import org.broadinstitute.barclay.argparser.Advanced;
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import org.broadinstitute.barclay.argparser.Hidden;
@@ -83,9 +84,9 @@ public class ExtractFingerprint extends CommandLineProgram {
     public boolean TEST_INPUT_READABILITY = true;
 
 
-    @Hidden
-    @Argument(doc = "When false, code will extract variants for every snp in the haplotype database, not only the representative one.")
-    public boolean EXTRACT_REPRESENTATIVES_ONLY = true;
+    @Advanced
+    @Argument(doc = "When true, code will extract variants for every snp in the haplotype database, not only the representative one.")
+    public boolean EXTRACT_NON_REPRESENTATIVES_TOO = false;
 
     @Override
     protected boolean requiresReference() {
@@ -139,7 +140,7 @@ protected int doWork() {
 
         try {
             FingerprintUtils.writeFingerPrint(soleEntry.getValue(), OUTPUT, referenceSequence.getReferenceFile(),
-                    sampleToUse, "PLs derived from " + INPUT + " using an assumed contamination of " + this.CONTAMINATION, EXTRACT_REPRESENTATIVES_ONLY);
+                    sampleToUse, "PLs derived from " + INPUT + " using an assumed contamination of " + this.CONTAMINATION, !EXTRACT_NON_REPRESENTATIVES_TOO);
         } catch (Exception e) {
             log.error(e);
         }

diff --git a/src/main/java/picard/fingerprint/FingerprintUtils.java b/src/main/java/picard/fingerprint/FingerprintUtils.java
@@ -147,8 +147,8 @@ public static VariantContextSet createVCSetFromFingerprint(final Fingerprint fin
     static Stream<VariantContext> getVariantContext(final ReferenceSequenceFile reference,
                                                     final String sample,
                                                     final HaplotypeProbabilities haplotypeProbabilities,
-                                                    final boolean representative_only) {
-        if (representative_only) {
+                                                    final boolean representativeOnly) {
+        if (representativeOnly) {
             return Stream.of(getVariantContextFromSnp(reference, sample, haplotypeProbabilities, haplotypeProbabilities.getRepresentativeSnp()));
         } else {
             return haplotypeProbabilities.getHaplotype().getSnps().stream().map(snp -> getVariantContextFromSnp(reference, sample, haplotypeProbabilities, snp));

diff --git a/src/test/java/picard/fingerprint/FingerprintCheckerTest.java b/src/test/java/picard/fingerprint/FingerprintCheckerTest.java
@@ -380,6 +380,7 @@ void testCanHandleDeepData(final HaplotypeProbabilitiesFromSequence hp, final in
         }
     }
 
+
     @DataProvider()
     Object[][] mergeIsSafeProvider() {
         final HaplotypeProbabilitiesFromSequence hp1 = new HaplotypeProbabilitiesFromSequence(hb);
-Original file line number
+Diff line change
@@ Expand Up @@
             }
         }
         @DataProvider()
         Object[][] mergeIsSafeProvider() {
             final HaplotypeProbabilitiesFromSequence hp1 = new HaplotypeProbabilitiesFromSequence(hb);
@@ Expand Down @@