From 231d3053eda2845feac7124261d37dc1e70aa595 Mon Sep 17 00:00:00 2001
From: ldgauthier <gauthier@broadinstitute.org>
Date: Thu, 21 Nov 2019 12:25:59 -0500
Subject: [PATCH] GatherTranches: fix required arg that had a default value,
 making it not required anymore (#6273)

---
 .../tools/walkers/vqsr/GatherTranches.java    |  4 ++--
 .../vqsr/GatherTranchesIntegrationTest.java   | 20 +++++++++++++++++++
 .../VQSR/expected/indels.gathered.tranches    |  3 +++
 .../resources/large/VQSR/indels.0.tranches    |  3 +++
 .../resources/large/VQSR/indels.1.tranches    |  3 +++
 5 files changed, 31 insertions(+), 2 deletions(-)
 create mode 100644 src/test/resources/large/VQSR/expected/indels.gathered.tranches
 create mode 100644 src/test/resources/large/VQSR/indels.0.tranches
 create mode 100644 src/test/resources/large/VQSR/indels.1.tranches

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/GatherTranches.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/GatherTranches.java
index c01d13493ba..b836bcd8940 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/GatherTranches.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/GatherTranches.java
@@ -43,8 +43,8 @@ public class GatherTranches extends CommandLineProgram {
     /**
      * Use either SNP for recalibrating only SNPs (emitting indels untouched in the output VCF) or INDEL for indels (emitting SNPs untouched in the output VCF). There is also a BOTH option for recalibrating both SNPs and indels simultaneously, but this is meant for testing purposes only and should not be used in actual analyses.
      */
-    @Argument(fullName = "mode", shortName = "mode", doc = "Recalibration mode to employ", optional = false)
-    public VariantRecalibratorArgumentCollection.Mode MODE = VariantRecalibratorArgumentCollection.Mode.SNP;
+    @Argument(fullName = "mode", shortName = "mode", doc = "Recalibration mode to employ")
+    public VariantRecalibratorArgumentCollection.Mode MODE;
 
     @Argument(fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME,
             shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME, doc="File to output the gathered tranches file to")
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/GatherTranchesIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/GatherTranchesIntegrationTest.java
index 2c503b2f9a5..10a322f0731 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/GatherTranchesIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/GatherTranchesIntegrationTest.java
@@ -28,6 +28,7 @@ public void testCombine2Shards() throws Exception {
         args.add(recal1.getAbsolutePath());
         args.add("--input");
         args.add(recal2.getAbsolutePath());
+        args.addArgument("mode", "SNP");
 
         final File outFile = GATKBaseTest.createTempFile("gatheredTranches", ".txt");
         args.addOutput(outFile);
@@ -36,5 +37,24 @@ public void testCombine2Shards() throws Exception {
         IntegrationTestSpec.assertEqualTextFiles(outFile, recal_original);
     }
 
+    @Test
+    public void testCombine2IndelTranches() throws Exception {
+        final File tranches1 = new File(testDir + "indels.0.tranches");
+        final File tranches2 = new File(testDir + "indels.1.tranches");
+
+        final File recal_original = new File(testDir + "expected/indels.gathered.tranches");
+
+        final ArgumentsBuilder args = new ArgumentsBuilder();
+        args.add("--input");
+        args.add(tranches1.getAbsolutePath());
+        args.add("--input");
+        args.add(tranches2.getAbsolutePath());
+        args.addArgument("mode", "INDEL");
 
+        final File outFile = GATKBaseTest.createTempFile("gatheredTranches", ".txt");
+        args.addOutput(outFile);
+        final Object res = this.runCommandLine(args.getArgsArray());
+        Assert.assertEquals(res, 0);
+        IntegrationTestSpec.assertEqualTextFiles(outFile, recal_original);
+    }
 }
\ No newline at end of file
diff --git a/src/test/resources/large/VQSR/expected/indels.gathered.tranches b/src/test/resources/large/VQSR/expected/indels.gathered.tranches
new file mode 100644
index 00000000000..e6a038ea28e
--- /dev/null
+++ b/src/test/resources/large/VQSR/expected/indels.gathered.tranches
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e1c011564551ef6d323a56c6ef45758a818c408616a1ba18daad2e864166efe4
+size 476
diff --git a/src/test/resources/large/VQSR/indels.0.tranches b/src/test/resources/large/VQSR/indels.0.tranches
new file mode 100644
index 00000000000..50f4439c74f
--- /dev/null
+++ b/src/test/resources/large/VQSR/indels.0.tranches
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:15711d2da31952cd0207a935d0e1f80f5445cf2bf76f9e55fec4719ca575633f
+size 99338
diff --git a/src/test/resources/large/VQSR/indels.1.tranches b/src/test/resources/large/VQSR/indels.1.tranches
new file mode 100644
index 00000000000..49723e790a9
--- /dev/null
+++ b/src/test/resources/large/VQSR/indels.1.tranches
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:99ecdf1ff97e926e295b8af9da2a22b9fa436d1a1fdbcd20dd41fe40399228f9
+size 99252