-- The NanoSchedule timing code (in NSRuntimeProfile) was crazy expensive, but never showed up in the profilers. Removed all of the timing code from the NanoScheduler, the NSRuntimeProfile itself, and updated the unit tests.
-- For tools that largely pass through data quickly, this change reduces runtimes by as much as 10x. For the RealignerTargetCreator example, the runtime before this commit was 3 hours, and after is 30 minutes (6x improvement).
-- Took this opportunity to improve the GATK ProgressMeter. NotifyOfProgress now just keeps track of the maximum position seen, and a separate daemon thread ProgressMeterDaemon periodically wakes up and prints the current progress. This removes all inner loop calls to the GATK timers.
-- The history of the bug started here: http://gatkforums.broadinstitute.org/discussion/comment/2402#Comment_2402
-- The previous nanoscheduler would deadlock in the case where an Error, not an Exception, was thrown. Errors, like out of memory, would cause the whole system to die. This bugfix resolves that issue
The check is performed by a Read Transformer that samples (currently set to once
every 1000 reads so that we don't hurt overall GATK performance) from the input
reads and checks to make sure that none of the base quals is too high (> Q60). If
we encounter such a base then we fail with a User Error.
* Can be over-ridden with --allow_potentially_misencoded_quality_scores.
* Also, the user can choose to fix his quals on the fly (presumably using PrintReads
to write out a fixed bam) with the --fix_misencoded_quality_scores argument.
Added unit tests.
-- Wasn't handling indel overlaps correctly in SiteIterator.getSitesBefore, causing it to incorrectly skip variants underlying indels (the getSitesBefore was considering both start and stop [not the correct behavior]) causing it to only get sites up to the first record whose stop overlapped the requested start.
-- Just separated infrastructure into core package, away from the walkers themselves.
-- Added na12878kb.jar target that builds a jar that can run a test main function (see testNA12878kbJar.csh)
-Allows packaged resource files to be accessed within tests
-Guards against packaging errors in dist/ jars by testing the
jars that actually get run rather than unpackaged class files.
Previously we were only protected against packaging errors in the
monolithic jars posted to our website, not the dist/ jars used in
everyday runs.
-"ant fasttest" still uses the unpackaged class files for speed
(don't want to have to rebuild the jars in fasttest). Relies on
dubious methods to get at the resource files that would end up
in the jars.
-Eliminated the stupid separate "test" ivy config. Now we only
invoke ivy ONCE during an ant build that includes tests.
Mark DePristo
Mauricio Carneiro
Eric Banks
Randal Moore
Menachem Fromer
Ryan Poplin
Jacob Silterra
Joel Thibault
Johan Dahlberg
David Roazen