ReadSparkSource.getHeader silently manufactures a bogus SAMFileHeader for ADAM (and possibly other) files

[cmnbroad]

And probably other kinds of files too. The stack below results from handing it a .ADAM file in the MeanQualityByCycleSparkIntegrationTest.test_ADAM test. The ReadSparkSource code is currently delegating to Hadoop-BAM, which is in turn delegating to promiscuous htsjdk code that says anything that doesn't look like known file type must be a SAM file. It then happily creates a bogus SAMFileHeader from the .ADAM stream.

All 3 layers should probably be more discriminating.

This currently doesn't break any tests. I discovered it when running the HB tests against a local version of htsjdk with a strict setHeader implementation that attempts to resolve all reference names on every setHeader call. That code caused this test to fail because its using the bogus header.

"main@1" prio=5 tid=0x1 nid=NA runnable
java.lang.Thread.State: RUNNABLE
at htsjdk.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:113)
at htsjdk.samtools.SAMTextReader.readHeader(SAMTextReader.java:200)
at htsjdk.samtools.SAMTextReader.(SAMTextReader.java:63)
at htsjdk.samtools.SAMTextReader.(SAMTextReader.java:73)
at htsjdk.samtools.SAMFileReader.init(SAMFileReader.java:684)
at htsjdk.samtools.SAMFileReader.(SAMFileReader.java:148)
at org.seqdoop.hadoop_bam.util.SAMHeaderReader.readSAMHeaderFrom(SAMHeaderReader.java:66)
at org.seqdoop.hadoop_bam.util.SAMHeaderReader.readSAMHeaderFrom(SAMHeaderReader.java:47)
at org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource.getHeader(ReadsSparkSource.java:195)
at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReads(GATKSparkTool.java:284)
at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:264)
at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:255)
at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:36)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:98)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:146)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:165)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:66)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:73)
at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:68)
at org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MeanQualityByCycleSparkIntegrationTest.test_ADAM(MeanQualityByCycleSparkIntegrationTest.java:96)
at sun.reflect.NativeMethodAccessorImpl.invoke0(NativeMethodAccessorImpl.java:-1)
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:639)
at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:821)
at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1131)
at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
at org.testng.TestRunner.privateRun(TestRunner.java:773)
at org.testng.TestRunner.run(TestRunner.java:623)
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:1185)
at org.testng.TestNG.runSuitesLocally(TestNG.java:1110)
at org.testng.TestNG.run(TestNG.java:1018)
at org.testng.IDEARemoteTestNG.run(IDEARemoteTestNG.java:72)
at org.testng.RemoteTestNGStarter.main(RemoteTestNGStarter.java:122)