From 6d5556939d6835abcd99c02225d3ecb9518688f7 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 9 Jun 2010 01:47:04 +0000
Subject: [PATCH] updating Tribble with a couple of important Tabix fixes, and
 updating the variant eval integration tests to run each test with both plain
 vcf and gzipped tabix (added the tabix version to the vlidation directory),
 using the same md5sum.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3509 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../VariantEvalIntegrationTest.java           |  60 +++++++++++-------
 settings/repository/org.broad/tribble-88.xml  |   3 -
 .../{tribble-88.jar => tribble-98.jar}        | Bin 219967 -> 219933 bytes
 settings/repository/org.broad/tribble-98.xml  |   3 +
 4 files changed, 41 insertions(+), 25 deletions(-)
 delete mode 100644 settings/repository/org.broad/tribble-88.xml
 rename settings/repository/org.broad/{tribble-88.jar => tribble-98.jar} (88%)
 create mode 100644 settings/repository/org.broad/tribble-98.xml

diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
index 1b4392fbf..28fa4b262 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
@@ -17,13 +17,21 @@ public class
             " -B eval,VCF," + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
             " -B comp_genotypes,VCF," + validationDataLocation + "yri.trio.gatk.ug.head.vcf -reportType Grep";
 
+    private static String rootGZ = cmdRoot +
+                " -D " + GATKDataLocation + "dbsnp_129_b36.rod" +
+                " -B eval,VCF," + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf.gz" +
+                " -B comp_genotypes,VCF," + validationDataLocation + "yri.trio.gatk.ug.head.vcf.gz -reportType Grep";
+
+    private static String[] testsEnumerations = {root, rootGZ};
 
     @Test
     public void testSelect1() {
         String extraArgs = "-L 1:1-10,000,000";
-        WalkerTestSpec spec = new WalkerTestSpec( withSelect(root, "DP < 50", "DP50") + " " + extraArgs + " -o %s",
-                1, Arrays.asList("5a330d359b5c7ea0dfa6698b4830db82"));
-        executeTest("testSelect1", spec);
+        for (String tests : testsEnumerations) {
+            WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -o %s",
+                    1, Arrays.asList("5a330d359b5c7ea0dfa6698b4830db82"));
+            executeTest("testSelect1", spec);
+        }
     }
 
     @Test
@@ -36,10 +44,14 @@ public class
 
     @Test
     public void testVEGenotypeConcordance() {
-        WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -B eval,VCF," + validationDataLocation + "GenotypeConcordanceEval.vcf -B comp,VCF," + validationDataLocation + "GenotypeConcordanceComp.vcf -E GenotypeConcordance -reportType CSV -o %s",
-                1, // just one output file
-                Arrays.asList("608b32189818df7271c546dd5f257033"));
-        executeTest("testVEGenotypeConcordance", spec);
+        String vcfFiles[] = {"GenotypeConcordanceEval.vcf", "GenotypeConcordanceEval.vcf.gz"};
+        for (String vcfFile : vcfFiles) {
+            WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -B eval,VCF," + validationDataLocation + vcfFile + " -B comp,VCF," + validationDataLocation + "GenotypeConcordanceComp.vcf -E GenotypeConcordance -reportType CSV -o %s",
+                    1,
+                    Arrays.asList("608b32189818df7271c546dd5f257033"));
+            executeTest("testVEGenotypeConcordance" + vcfFile, spec);
+        }
+
     }
 
     @Test
@@ -51,11 +63,12 @@ public class
         for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
             String extraArgs = entry.getKey();
             String md5 = entry.getValue();
-
-            WalkerTestSpec spec = new WalkerTestSpec( root + " " + extraArgs + " -o %s",
+            for (String tests : testsEnumerations) {
+                WalkerTestSpec spec = new WalkerTestSpec( tests + " " + extraArgs + " -o %s",
                     1, // just one output file
                     Arrays.asList(md5));
-            executeTest("testVESimple", spec);
+                executeTest("testVESimple", spec);
+            }
         }
     }
 
@@ -71,25 +84,28 @@ public class
         expectations.put("", matchingMD5);
         expectations.put(" -known comp_hapmap -known dbsnp", matchingMD5);
         expectations.put(" -known comp_hapmap", "fd9cd9970f7e509ca476502869063929");
+        for (String tests : testsEnumerations) {
+            for (Map.Entry<String, String> entry : expectations.entrySet()) {
+                String extraArgs2 = entry.getKey();
+                String md5 = entry.getValue();
 
-        for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
-            String extraArgs2 = entry.getKey();
-            String md5 = entry.getValue();
-
-            WalkerTestSpec spec = new WalkerTestSpec( root + " " + extraArgs1 + extraArgs2 + " -o %s",
-                    1, // just one output file
-                    Arrays.asList(md5));
-            executeTest("testVEComplex", spec);
+                WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs1 + extraArgs2 + " -o %s",
+                        1, // just one output file
+                        Arrays.asList(md5));
+                executeTest("testVEComplex", spec);
+            }
         }
     }
 
     @Test
     public void testVEWriteVCF() {
         String extraArgs = "-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 30";
-        WalkerTestSpec spec = new WalkerTestSpec( root + " " + extraArgs + " -o %s -outputVCF %s",
-                2,
-                Arrays.asList("521837758da151b84fca57fd1bb7dad1", "b4a42c90318adc88361691ece50426f2"));
-        executeTest("testVEWriteVCF", spec);
+        for (String tests : testsEnumerations) {
+            WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs + " -o %s -outputVCF %s",
+                    2,
+                    Arrays.asList("521837758da151b84fca57fd1bb7dad1", "b4a42c90318adc88361691ece50426f2"));
+            executeTest("testVEWriteVCF", spec);
+        }
     }
 
     private static String withSelect(String cmd, String select, String name) {
diff --git a/settings/repository/org.broad/tribble-88.xml b/settings/repository/org.broad/tribble-88.xml
deleted file mode 100644
index 1c14d8043..000000000
--- a/settings/repository/org.broad/tribble-88.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="88" status="integration" publication="20100603124200" />
-</ivy-module>
diff --git a/settings/repository/org.broad/tribble-88.jar b/settings/repository/org.broad/tribble-98.jar
similarity index 88%
rename from settings/repository/org.broad/tribble-88.jar
rename to settings/repository/org.broad/tribble-98.jar
index 6786642fdb4f1769179e4118ab3c0ffe97211a2f..9e5225ab1baef39d41ae67aa97856ae50e156d83 100644
GIT binary patch
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diff --git a/settings/repository/org.broad/tribble-98.xml b/settings/repository/org.broad/tribble-98.xml
new file mode 100644
index 000000000..625b974fe
--- /dev/null
+++ b/settings/repository/org.broad/tribble-98.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="org.broad" module="tribble" revision="98" status="integration" publication="20100608124200" />
+</ivy-module>