Fixed integration test expected data generation test.

Regenerated integration test expected.

Author: jonn-smith

src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java

@@ -34,6 +34,7 @@
 import java.io.*;
 import java.nio.file.Files;
 import java.nio.file.Paths;
+import java.nio.file.StandardCopyOption;
 import java.util.*;
 import java.util.stream.Collectors;
 import java.util.stream.IntStream;
@@ -116,7 +117,7 @@ public class FuncotatorIntegrationTest extends CommandLineProgramTest {
     //==================================================================================================================
     // Disabled tests to regenerate expected outputs for integration tests:
     @Test(dataProvider = "provideForNonTrivialLargeDataValidationTest",
-            enabled = false)
+               enabled = false)
     public void regenerateExpectedOutputsForNonTrivialLargeDataValidationTest(
                                                   final String inputVcfName,
                                                   final String referencePath,
@@ -146,7 +147,7 @@ public void regenerateExpectedOutputsForNonTrivialLargeDataValidationTest(
 
             // Copy the output file to our expected output area:
             try {
-                Files.copy(outputFile.toPath(), IOUtils.getPath(typeCorrectedExpectedOutputPath));
+                Files.copy(outputFile.toPath(), IOUtils.getPath(typeCorrectedExpectedOutputPath), StandardCopyOption.REPLACE_EXISTING);
             }
             catch ( final IOException ex ) {
                 throw new GATKException("Unable to copy over generated data to expected output path!", ex);

src/test/resources/large/funcotator/regressionTestHg19Large_expected.maf

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:5896c6f18555dafad10a63e78e57aed58a7e9166a526d9faccad2460064f0425
-size 1063240
+oid sha256:0f8d14830c557c3db7c36587f868337b57f5d1f38df62c31c839710033482bfc
+size 1064190

src/test/resources/large/funcotator/regressionTestHg19Large_expected.vcf

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:8e3b09bb68652b0442acd0c7316d475cd2431d084c0a93a256b38d9c455fccb8
-size 440190
+oid sha256:82f59d0e0c139e7f3612434837b8646582c73a5f8d829a0fd0d85e804fd6b269
+size 441140

src/test/resources/large/funcotator/regressionTestVariantSet1_expected.maf

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:a3b64bcd907cd33003660f2bbe3b10e38bf7a08d039daa35e0bda1498b0e3e91
-size 155319
+oid sha256:6c2978ef6b685316dd12887955ade63ffbd158d43dc45cb87163a7ef4e80dc1a
+size 155612

src/test/resources/large/funcotator/regressionTestVariantSet1_expected.vcf

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:ba5c580eb0c17689c49a238b0b4e00075ee145eca96bf2ee45769bd98ac8d2ce
-size 80367
+oid sha256:a0c337c5d29df10db771578eb26faa0f4ce5400fa91213c0b97e2e54bd104a8d
+size 80661

src/test/resources/large/funcotator/regressionTestVariantSet2_expected.maf

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:bc6b4494db85020773fa7ef336ba4577222b9de6e8c87489bcfb52e4120e2242
-size 130451
+oid sha256:48dd7e7cf36b82db74bde7f5d1d7d86fc33e72f45d3b14781484f2cfbb2091d0
+size 130964

src/test/resources/large/funcotator/regressionTestVariantSet2_expected.vcf

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:f244981f8f1f0057c96019382dfc8149fbaf5eeea3d06c46e85399d791c90604
-size 68684
+oid sha256:ff4ba2bdfd4d57e01bde74084761d3b6baf62da4672775d32c53efc40cbb6e45
+size 69198

src/test/resources/large/funcotator/regressionTestVariantSetHG38_expected.maf

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:18ae7086f55fa15001ef50cfca656331415db53a05d4f452575f9a6bd8ea181c
-size 199520
+oid sha256:717061b2ee29f09a1be8c23834869a91524021c08b6de3194521dfe241cfffe4
+size 199638

src/test/resources/large/funcotator/regressionTestVariantSetHG38_expected.vcf

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:47e13d5cfcc2f972c4b339ca6ade935280ad4aead20c741a77363f018508a4a6
-size 191760
+oid sha256:288430164c4ef986f173bdfc9b5b07188ccb5707d3998e0774897b8287520a10
+size 191879