diff --git a/public/external-example/pom.xml b/public/external-example/pom.xml
index fea1e93e3..c4c8a691c 100644
--- a/public/external-example/pom.xml
+++ b/public/external-example/pom.xml
@@ -204,10 +204,6 @@
**/*UnitTest.class
-
- ${gatk.basedir}
- unit
-
@@ -240,10 +236,6 @@
**/*IntegrationTest.class
-
- ${gatk.basedir}
- integrationtest
-
diff --git a/public/gatk-root/pom.xml b/public/gatk-root/pom.xml
index a7e720acb..b0adc4cc9 100644
--- a/public/gatk-root/pom.xml
+++ b/public/gatk-root/pom.xml
@@ -424,10 +424,6 @@
**/*UnitTest.class
-
- ${gatk.basedir}
- unit
-
@@ -478,10 +474,6 @@
**/*IntegrationTest.class
-
- ${gatk.basedir}
- integration
-
@@ -499,10 +491,6 @@
**/*QueueTest.class
-
- ${gatk.basedir}
- queue
-
@@ -519,10 +507,6 @@
**/*LargeScaleTest.class
-
- ${gatk.basedir}
- largescale
-
@@ -539,10 +523,6 @@
**/*KnowledgeBaseTest.class
-
- ${gatk.basedir}
- knowledgebasetests
-
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java
index 0f73d9002..1c78574df 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java
@@ -88,10 +88,7 @@ public abstract class BaseTest {
public static final Logger logger = CommandLineUtils.getStingLogger();
private static final String CURRENT_DIRECTORY = System.getProperty("user.dir");
- public static final String gatkDirectory = System.getProperty("gatkdir", CURRENT_DIRECTORY) + "/";
public static final String baseDirectory = System.getProperty("basedir", CURRENT_DIRECTORY) + "/";
- public static final String testType = System.getProperty("testType"); // May be null
- public static final String testTypeSubDirectory = testType == null ? "" : ("/" + testType); // May be empty
public static final String hg18Reference = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
public static final String hg19Reference = "/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta";
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java
index 0313ad3e9..218906fdd 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java
@@ -49,7 +49,7 @@ public class MD5DB {
*/
private static final int MAX_RECORDS_TO_READ = 1000000;
private static final int MAX_RAW_DIFFS_TO_SUMMARIZE = -1;
- public static final String LOCAL_MD5_DB_DIR = BaseTest.gatkDirectory + "integrationtests";
+ public static final String LOCAL_MD5_DB_DIR = BaseTest.baseDirectory + "integrationtests";
public static final String GLOBAL_MD5_DB_DIR = "/humgen/gsa-hpprojects/GATK/data/integrationtests";
// tracking and emitting a data file of origina and new md5s
@@ -65,26 +65,14 @@ public class MD5DB {
ensureMd5DbDirectory();
- boolean exists = MD5MismatchesFile.exists();
-
- if (!exists) {
- logger.warn("Creating md5 mismatch db at " + MD5MismatchesFile);
- } else {
- logger.warn("Updating md5 mismatch db at " + MD5MismatchesFile);
- }
- logger.warn("GATK directory: " + BaseTest.gatkDirectory);
- logger.warn("Base directory: " + BaseTest.baseDirectory);
- logger.warn("Test type: " + BaseTest.testType);
-
+ logger.debug("Creating md5 mismatch db at " + MD5MismatchesFile);
try {
- md5MismatchStream = new PrintStream(new FileOutputStream(MD5MismatchesFile, true));
+ md5MismatchStream = new PrintStream(new FileOutputStream(MD5MismatchesFile));
+ md5MismatchStream.printf("%s\t%s\t%s%n", "expected", "observed", "test");
} catch ( FileNotFoundException e ) {
throw new ReviewedGATKException("Failed to open md5 mismatch file", e);
}
- if (!exists) {
- md5MismatchStream.printf("%s\t%s\t%s%n", "expected", "observed", "test");
- }
}
public void close() {