-Make MaxRuntimeIntegrationTest more lenient by assuming that startup overhead
might be as long as 120 seconds on a very slow node, rather than the original
assumption of 20 seconds
-In TraverseActiveRegionsUnitTest, write temp bam file to the temp directory, not
to the current working directory
-SimpleTimerUnitTest: This test was internally inconsistent. It asserted that
a particular operation should take no more than 10 milliseconds, and then asserted
again that this same operation should take no more than 100 microseconds (= 0.1 millisecond).
On a slow node it could take slightly longer than 100 microseconds, however.
Changed the test to assert that the operation should require no more than 10000 microseconds
(= 10 milliseconds)
-change global default test timeout from 20 to 40 minutes (things just take longer
on the farm!)
-build.xml: allow runtestonly target to work with scala test classes
-replace unnecessary uses of the UnifiedGenotyper by public integration tests
with PrintReads
-move NanoSchedulerIntegrationTest to protected, since it's completely dependent
on the UnifiedGenotyper
-- Providing this optional argument -maxRuntime (in -maxRuntimeUnits units) causes the GATK to exit gracefully when the max. runtime has been exceeded. By cleanly I mean that the engine simply stops at the next available cycle in the walker as through the end of processing had been reached. This means that all output files are closed properly, etc.
-- Emits an info message that looks like "INFO 10:36:52,723 MicroScheduler - Aborting execution (cleanly) because the runtime has exceeded the requested maximum 10.0000 s". Otherwise there's currently no way to differentiate a truly completed run from a timelimit exceeded run, which may be a useful thing for a future update
-- Resolves GSA-630 / GATK max runtime to deal with bad LSA calling?
-- Added new JIRA entry for Ami to restart chr1 macarthur with this argument set to -maxRuntime 1 -maxRuntimeUnits DAYS to see if we can do all of chr1 in one weekend.
David Roazen
Mauricio Carneiro
Mark DePristo