This is an intermediate commit so that there is a record of these changes in our
commit history. Next step is to isolate the test classes as well, and then move
the entire package to the Picard repository and replace it with a jar in our repo.
-Removed all dependencies on org.broadinstitute.sting (still need to do the test classes,
though)
-Had to split some of the utility classes into "GATK-specific" vs generic methods
(eg., GATKVCFUtils vs. VCFUtils)
-Placement of some methods and choice of exception classes to replace the StingExceptions
and UserExceptions may need to be tweaked until everyone is happy, but this can be
done after the move.
-- Now each map job reads a value, performs map, and does as much reducing as possible. This ensures that we scale performance with the nct value, so -nct 2 should result in 2x performance, -nct 3 3x, etc. All of this is accomplished using exactly NCT% of the CPU of the machine.
-- Has the additional value of actually simplifying the code
-- Resolves a long-standing annoyance with the nano scheduler.
-Switch back to the old implementation, if needed, with --use_legacy_downsampler
-LocusIteratorByStateExperimental becomes the new LocusIteratorByState, and
the original LocusIteratorByState becomes LegacyLocusIteratorByState
-Similarly, the ExperimentalReadShardBalancer becomes the new ReadShardBalancer,
with the old one renamed to LegacyReadShardBalancer
-Performance improvements: locus traversals used to be 20% slower in the new
downsampling implementation, now they are roughly the same speed.
-Tests show a very high level of concordance with UG calls from the previous
implementation, with some new calls and edge cases that still require more examination.
-With the new implementation, can now use -dcov with ReadWalkers to set a limit
on the max # of reads per alignment start position per sample. Appropriate value
for ReadWalker dcov may be in the single digits for some tools, but this too
requires more investigation.
-- 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.
-- Multi-allelic variants are split into their bi-allelic version, trimmed, and we attempt to provide a meaningful genotype for NA12878 here. It's not perfect and needs some discussion on how to handle het/alt variants
-- Adding splitInBiallelic funtion to VariantContextUtils as well as extensive unit tests that also indirectly test reverseTrimAlleles (which worked perfectly FYI)
-- Closes GSA-494 / Add maximum runtime for integration tests, running them in timeout thread
-- Needed to debug locking issues
-- Needed to debug excessively long running integrationtests
-- Added build.xml maximum runtime for all testng tests of 10 hours. We will ultimately fail the build if it goes on for more than 10 hours
-- The logic for determining active regions was a bit broken in the HC when intervals were used in the system
-- TraverseActiveRegions now uses the AllLocus view, since we always want to see all reference sites, not just those covered. Simplifies logic of TAR
-- Non-overlapping intervals are always treated as separate objects for determing active / inactive state. This means that each exon will stand on its own when deciding if it should be active or inactive
-- Misc. cleanup, docs of some TAR infrastructure to make it safer and easier to debug in the future.
-- Committing the SingleExomeCalling script that I used to find this problem, and will continue to use in evaluating calling of a single exome with the HC
-- Make sure to get all of the reads into the set of potentially active reads, even for genomic locations that themselves don't overlap the engine intervals but may have reads that overlap the regions
-- Remove excessively expensive calls to check bases are upper cased in ReferenceContext
-- Update md5s after a lot of manual review and discussion with Ryan
-- As one might expect, CachingIndexedFastaSequenceFile now internally upper cases the FASTA reference bases. This is now done by default, unless requested explicitly to preserve the original bases.
-- This is really the correct place to do this for a variety of reasons. First, you don't need to work about upper casing bases throughout the code. Second, the cache is only upper cased once, no matter how often the bases are accessed, which walkers cannot optimize themselves. Finally, this uses the fastest function for this -- Picard's toUpperCase(byte[]) which is way better than String.toUpperCase()
-- Added unit tests to ensure this functionality works correct.
-- Removing unnecessary upper casing of bases in some core GATK tools, now that RefContext guarentees that the reference bases are all upper case.
-- Added contracts to ensure this is the case.
-- Remove a ton of sh*t from BaseUtils that was so old I had no idea what it was doing any longer, and didn't have any unit tests to ensure it was correct, and wasn't used anywhere in our code
David Roazen
Mark DePristo
Joel Thibault
Yossi Farjoun
Eric Banks
Ami Levy-Moonshine