From 0f78f70ed44c005d5296a1da84da31ae772ba18e Mon Sep 17 00:00:00 2001 From: aaron Date: Tue, 10 Aug 2010 02:57:23 +0000 Subject: [PATCH] fix for feature source in Tribble; we need to check that the record coming back isn't null. Also in the GATK added code to set the default logging level in integration tests to WARN, with the default level change they were spewing a bunch of text. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3995 348d0f76-0448-11de-a6fe-93d51630548a --- java/test/org/broadinstitute/sting/WalkerTest.java | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/java/test/org/broadinstitute/sting/WalkerTest.java b/java/test/org/broadinstitute/sting/WalkerTest.java index aa1391447..f090c7b52 100755 --- a/java/test/org/broadinstitute/sting/WalkerTest.java +++ b/java/test/org/broadinstitute/sting/WalkerTest.java @@ -271,8 +271,16 @@ public class WalkerTest extends BaseTest { command = cmd2; } System.out.println(String.format("Executing test %s with GATK arguments: %s", name, Utils.join(" ",command))); - CommandLineExecutable.start(instance, command); + // add the logging level to each of the integration test commands + String[] cmd2 = Arrays.copyOf(command, command.length + 2); + cmd2[command.length] = "-l"; + cmd2[command.length+1] = "WARN"; + + // run the executable + CommandLineExecutable.start(instance, cmd2); + + // catch failures from the integration test if (CommandLineExecutable.result != 0) { throw new RuntimeException("Error running the GATK with arguments: " + args); }