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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
This commit is contained in:
aaron 2010-08-10 02:57:23 +00:00
parent 419a36f74c
commit 0f78f70ed4
1 changed files with 9 additions and 1 deletions
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10
java/test/org/broadinstitute/sting/WalkerTest.java
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@ -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);
}