Fix the warning about Vfs.dir when registering genomics coders

[akiezun]

From @lbergelson on July 1, 2015 18:47

Some (but not all) users get a warning whenever they run a dataflow pipeline that calls DataflowWorkarounds.registerGenomicsCoders

Here is an example:

Jul 01, 2015 2:33:36 PM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coders for genomics classes
Jul 01, 2015 2:33:36 PM org.reflections.Reflections scan
WARNING: could not create Vfs.Dir from url. ignoring the exception and continuing
org.reflections.ReflectionsException: could not create Vfs.Dir from url, no matching UrlType was found [file:/Library/KeyAccess/KeyAccess.app/Contents/SharedFrameworks/KeyAccess.framework/KeyAccess]
either use fromURL(final URL url, final List<UrlType> urlTypes) or use the static setDefaultURLTypes(final List<UrlType> urlTypes) or addDefaultURLTypes(UrlType urlType) with your specialized UrlType.
    at org.reflections.vfs.Vfs.fromURL(Vfs.java:109)
    at org.reflections.vfs.Vfs.fromURL(Vfs.java:91)
    at org.reflections.Reflections.scan(Reflections.java:237)
    at org.reflections.Reflections.scan(Reflections.java:204)
    at org.reflections.Reflections.<init>(Reflections.java:129)
    at com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds.registerGenomicsCoders(DataflowWorkarounds.java:90)
    at org.broadinstitute.hellbender.tools.dataflow.transforms.InsertSizeMetricsTransformUnitTest.testInsertSizeMetricsTransform(InsertSizeMetricsTransformUnitTest.java:49)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
    at org.testng.internal.Invoker.invokeMethod(Invoker.java:659)
    at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:845)
    at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1153)
    at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:125)
    at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
    at org.testng.TestRunner.privateRun(TestRunner.java:771)
    at org.testng.TestRunner.run(TestRunner.java:621)
    at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
    at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
    at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
    at org.testng.SuiteRunner.run(SuiteRunner.java:259)
    at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
    at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
    at org.testng.TestNG.runSuitesSequentially(TestNG.java:1199)
    at org.testng.TestNG.runSuitesLocally(TestNG.java:1124)
    at org.testng.TestNG.run(TestNG.java:1032)
    at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:111)
    at org.testng.remote.RemoteTestNG.initAndRun(RemoteTestNG.java:204)
    at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:175)
    at org.testng.RemoteTestNGStarter.main(RemoteTestNGStarter.java:125)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at com.intellij.rt.execution.application.AppMain.main(AppMain.java:140)

Jul 01, 2015 2:33:37 PM org.reflections.Reflections scan

The fact that it doesn't show up for some users means its likely to be an environmental difference, possibly an underspecified dependency.

@davidaadams I understand that you never see this warning, could you confirm/deny that.

Copied from original issue: broadinstitute/hellbender#609