-- For the pooled caller we were writing diploid no-calls even when other samples were haploid. Changed maxPloidy function to return a defaultPloidy, rather than 0, in the case where all samples are missing.
-- VCF/BCF Writers now create missing genotypes with the ploidy of other samples, or 2 if none are available at all.
-- Updating integration tests for general ploidy, as previously we wrote ./. even when other calls were 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/1/1/1/1/1, but now we write ./././././././././././././././././././././././. (ugly but correct)
-- Previous code was looking for a -1 result from maxPloidy() but the result as actually 0, so instead of writing a diploid no call we were actually writing "unavailable" genotypes, and failing the BCF == VCF test in integration tests. Fixed.
-- Turns out this was consuming 30% of the UG runtime, and causing problems elsewhere.
-- Removed addMissingSamples from VariantcontextUtils, and calls to it
-- Updated VCF / BCF writers to automatically write out a diploid no call for missing samples
-- Added unit tests for this behavior in VariantContextWritersUnitTest
1) SelectVariants could throw a ReviewedStingException (one of the nasty "Bug:") ones if the user requested a sample that wasn't present in the VCF. The walker now
checks for this in the initialize() phase, and throws a more informative error if the situation is detected. If the user simply wants to subset the VCF to
all the samples requested that are actually present in the VCF, the --ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES flag changes this UserException to a Warning,
and does the appropriate subsetting. Added integration tests for this.
2) GenotypeLikelihoods has an unsafe method getLog10GQ(GenotypeType), which is completely broken for multi-allelic sites. I marked that method
as deprecated, and added methods that use the context of the allele ordering (either directly specified or as a VC) to retrieve the appropriate GQ, and
added a unit test to cover this case. VariantsToBinaryPed needs to dynamically calculate the GQ field sometimes (because I have some VCFs with PLs but no GQ).
-- Now prints out a single combined NanoScheduler runtime profile report across all nano schedulers in use. So now if you run with -nt 4 you'll get one combined NanoScheduler profiler across all 4 instances of the NanoScheduler within TraverseXNano.
-- Basically you cannot safely use instance specific ThreadLocal variables, as these cannot be safely cleaned up. The old implementation kept pointers to old writers, with huge tribble block indexes, and eventually we crashed out of integration tests
-- See http://weblogs.java.net/blog/jjviana/archive/2010/06/10/threadlocal-thread-pool-bad-idea-or-dealing-apparent-glassfish-memor for more information
-- New implementation uses a borrow/return schedule with a list of N TraversalEngines managed by the MicroScheduler directly.
-- Can now say -nt 4 and -nct 4 to get 16 threads running for you!
-- TraversalEngines are now ThreadLocal variables in the MicroScheduler.
-- Misc. code cleanup, final variables, some contracts.
-- TraversalProgressMeter now completely generalized, named ProgressMeter in utils.progressmeter. Now just takes "nRecordsProcessed" as an argument to print reads. Completely removes dependence on complex data structures from TraversalProgressMeter. Can be used to measure progress on any task with processing units in genomic locations.
-- a fairly simple, class with no dependency on GATK engine or other features.
-- Currently only used by the TraversalEngine / MicroScheduler but could be used for any purpose now, really.
-- Previously these core progress metering functions were all in TraversalEngine, and available to subclasses like TraverseLoci via inheritance. The problem here is that the upcoming data threads x cpu threads parallelism requires one master copy of the progress metering shared among all traversals, but multiple instantiations of traverse engines themselves.
-- Because the progress metering code has horrible anyway, I've refactored and vastly cleaned up and simplified all of these capabilities into TraversalProgressMeter class. I've simplified down the classes it uses to work (STILL SOME TODOs in there) so that it doesn't reach into the core GATK engine all the time. It should be possible to write some nice tests for it now. By making it its own class, it can protect itself from multi-threaded access with a single synchronized printProgress function instead of carrying around multiple lock objects as before
-- Cleaned up the start up of the progress meter. It's now handled when the meter is created, so each micro scheduler doesn't have to deal with proper initialization timing any longer
-- Simplified and made clear the interface for shutting down the traversal engines. There's no a shutdown method in TraversalEngine that's called once by the MicroScheduler when the entire traversing in over. Nano traversals now properly shut down (was subtle bug I undercovered here). The printing of on traversal done metering is now handled by MicroScheduler
-- The MicroScheduler holds the single master copy of the progress meter, and doles it out to the TraversalEngines (currently 1 but in future commit there will be N).
-- Added a nice function to GenomeAnalysisEngine that returns the regions we will be processing, either the intervals requested or the whole genome. Useful for progress meter but also probably for other infrastructure as well
-- Remove a lot of the sh*ting Bean interface getting and setting in MicroScheduler that's no longer useful. The generic bean is just a shell interface with nothing in it.
-- By removing a lot of these bean accessors and setters many things are now final that used to be dynamic.
This will prevent bugs from occurring when Vanilla make changes to the API
as described here: http://vanillaforums.com/blog/api#configuration
Based on the bug that broke the website Guide section on 9/6/12,
the GATKDocs posting system will probably break in the next release if
this is not applied as a bug fix.
-- I've rewritten the entire NS framework to use a producer / consumer model for input -> map and from map -> reduce. This is allowing us to scale reasonably efficiently up to 4 threads (see figure). Future work on the nano scheduler will be itemized in a separate JIRA entry.
-- Restructured the NS code for clarity. Docs everywhere.
-- This is considered version 1.0
-Off by default; engine fork isolates new code paths from old code paths,
so no integration tests change yet
-Experimental implementation is currently BROKEN due to a serious issue
involving file spans. No one can/should use the experimental features
until I've patched this issue.
-There are temporarily two independent versions of LocusIteratorByState.
Anyone changing one version should port the change to the other (if possible),
and anyone adding unit tests for one version should add the same unit tests
for the other (again, if possible). This situation will hopefully be extremely
temporary, and last only until the experimental implementation is proven.
-- The NanoScheduler is doing a good job at tracking important information like time spent in map/reduce/input etc.
-- Can be disabled with static boolean in MicroScheduler if we have problems
-- See GSA-515 Nanoscheduler GSA-549 Retire TraverseReads and TraverseLoci after testing confirms nano scheduler version in single threaded version is fine
-- Closes GSA-515 Nanoscheduler GSA-542 Good interface to nanoScheduler
-- Old -nt means dataThreads
-- New -cnt (--num_cpu_threads_per_data_thread) gives you n cpu threads for each data thread in the system
-- Cleanup logic for handling data and cpu threading in HMS, LMS, and MS
-- GATKRunReport reports the total number of threads in use by the GATK, not just the nt value
-- Removed the io,cpu tags for nt. Stupid system if you ask me. Cleaned up the GenomeAnalysisEngine and ThreadAllocation handling to be totally straightforward now
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Eric Banks
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