-ReadShardBalancer was printing out an extra "Loading BAM index data for next contig"
message at traversal end, which was confusing users and making the GATK look stupid.
Suppress the extraneous message, and reword the log messages to be less confusing.
-Improve log message output when initializing the shard iterator in GenomeAnalysisEngine.
Don't mention BAMs when the are none, and say "Preparing for traversal" rather than
mentioning the meaningless-for-users concept of "shard strategy"
-These log messages are needed because the operations they surround might take a
while under some circumstances, and the user should know that the GATK is actively
doing something rather than being hung.
-Throw a UserException if a Locus or ActiveRegion walker is run with -dcov < 200,
since low dcov values can result in problematic downsampling artifacts for locus-based
traversals.
-Read-based traversals continue to have no minimum for -dcov, since dcov for read traversals
controls the number of reads per alignment start position, and even a dcov value of 1 might
be safe/desirable in some circumstances.
-Also reorganize the global downsampling defaults so that they are specified as annotations
to the Walker, LocusWalker, and ActiveRegionWalker classes rather than as constants in the
DownsamplingMethod class.
-The default downsampling settings have not been changed: they are still -dcov 1000
for Locus and ActiveRegion walkers, and -dt NONE for all other walkers.
-- Started by Mark. Finished up by Ryan.
-- GGA mode still respected glm argument for SNP and INDEL models, so that you would silently fail to genotype indels at all if the -glm INDEL wasn't provided, but you'd still emit the sites, so you'd see records in the VCF but all alleles would be no calls.
-- https://www.pivotaltracker.com/story/show/48924339 for more information
-- [resolves#48924339]
Problem
--------
Diagnose Targets is outputting missing intervals to stdout if the argument -missing is not provided
Solution
--------
Make it NOT default to stdout
[Delivers #50386741]
BandedHMM
---------
-- An implementation of a linear runtime, linear memory usage banded logless PairHMM. Thought about 50% faster than current PairHMM, this implementation will be superceded by the GraphHMM when it becomes available. The implementation is being archived for future reference
Useful infrastructure changes
-----------------------------
-- Split PairHMM into a N2MemoryPairHMM that allows smarter implementation to not allocate the double[][] matrices if they don't want, which was previously occurring in the base class PairHMM
-- Added functionality (controlled by private static boolean) to write out likelihood call information to a file from inside of LikelihoodCalculationEngine for using in unit or performance testing. Added example of 100kb of data to private/testdata. Can be easily read in with the PairHMMTestData class.
-- PairHMM now tracks the number of possible cell evaluations, and the LoglessCachingPairHMM updates the nCellsEvaluated so we can see how many cells are saved by the caching calculation.
Don't map class to counts in the ReadMetrics (necessitating 2 HashMap lookups for every increment).
Instead, wrap the ReadFilters with a counting version and then set those counts only when updating global metrics.
-- Add() call had a misplaced map.put call, so that we were always putting the result of get() back into the map, when what we really intended was to only put the value back in if the original get() resulted in a null and so initialized the result
-- Previous version took a Collection<GATKSAMRecord> to remove, and called ArrayList.removeAll() on this collection to remove reads from the ActiveRegion. This can be very slow when there are lots of reads, as ArrayList.removeAll ultimately calls indexOf() that searches through the list calling equals() on each element. New version takes a set, and uses an iterator on the list to remove() from the iterator any read that is in the set. Given that we were already iterating over the list of reads to update the read span, this algorithm is actually simpler and faster than the previous one.
-- Update HaplotypeCaller filterReadsInRegion to use a Set not a List.
-- Expanded the unit tests a bit for ActiveRegion.removeAll
-- The previous version of PerReadAlleleLikelihoodMap only stored the alleles in an ArrayList, and used ArrayList.contains() to determine if an allele was already present in the map. This is very slow with many alleles. Now keeps both the ArrayList (for get() performance) and a Set of alleles for contains().
1. Don't clone the dataSource's metrics object (because then the engine won't continue to get updated counts)
2. Use the dataSource's metrics object in the CountingFilteringIterator and not the first shard's object!
3. Synchronize ReadMetrics.incrementMetrics to prevent race conditions.
Also:
* Make sure users realize that the read counts are approximate in the print outs.
* Removed a lot of unused cruft from the metrics object while I was in there.
* Added test to make sure that the ReadMetrics read count does not overflow ints.
* Added unit tests for traversal metrics (reads, loci, and active region traversals); these test counts of reads and records.
-- [Delivers #49876703]
-- Add integration test and test file
-- Update SymbolicAlleles combine variant tests, which was turning unfiltered records into PASS!
- Converted my old GATKBAMIndexText (within PileupWalkerIntegrationTest) to use a dataProvider
- Added two integration tests to test -outputInsertLength option
Bug fixes and missing interval functionality for Diagnose Targets
While the code seems fine, the complex parts of it are untested. This is probably fine for now, but private code can have a tendency to creep into the codebase once accepted. I would have preferred that unit test OR a big comment stating that the code is untested (and thus broken by Mark's rule).
It is with these cavets that I accept the pull request.
-- The previous implementation of the maxRuntime would require us to wait until all of the work was completed within a shard, which can be a substantial amount of work in the case of a locus walker with 16kb shards.
-- This implementation ensures that we exit from the traversal very soon after the max runtime is exceeded, without completely all of our work within the shard. This is done by updating all of the traversal engines to return false for hasNext() in the nano scheduled input provider. So as soon as the timeout is exceeeded, we stop generating additional data to process, and we only have to wait until the currently executing data processing unit (locus, read, active region) completes.
-- In order to implement this timeout efficiently at this fine scale, the progress meter now lives in the genome analysis engine, and the exceedsTimeout() call in the engine looks at a periodically updated runtime variable in the meter. This variable contains the elapsed runtime of the engine, but is updated by the progress meter daemon thread so that the engine doesn't call System.nanotime() in each cycle of the engine, which would be very expense. Instead we basically wait for the daemon to update this variable, and so our precision of timing out is limited by the update frequency of the daemon, which is on the order of every few hundred milliseconds, totally fine for a timeout.
-- Added integration tests to ensure that subshard timeouts are working properly
Problem
------
Diagnose Targets identifies holes in the coverage of a targetted experiment, but it only reports them doesn't list the actual missing loci
Solution
------
This commit implements an optional intervals file output listing the exact loci that did not pass filters
Itemized changes
--------------
* Cache callable statuses (to avoid recalculation)
* Add functionality to output missing intervals
* Implement new tool to qualify the missing intervals (QualifyMissingIntervals) by gc content, size, type of missing coverage and origin (coding sequence, intron, ...)
Problem
-------
When the interval had no reads, it was being sent to the VCF before the intervals that just got processed, therefore violating the sort order of the VCF.
Solution
--------
Use a linked hash map, and make the insertion and removal all happen in one place regardless of having reads or not. Since the input is ordered, the output has to be ordered as well.
Itemized changes
--------------
* Clean up code duplication in LocusStratification and SampleStratification
* Add number of uncovered sites and number of low covered sites to the VCF output.
* Add new VCF format fields
* Fix outputting multiple status when threshold is 0 (ratio must be GREATER THAN not equal to the threshold to get reported)
[fixes#48780333]
[fixes#48787311]
David Roazen
Mark DePristo
Mauricio Carneiro
Ryan Poplin
delangel
Eric Banks
Valentin Ruano Rubio
Yossi Farjoun
chartl
Chris Hartl