-- Separate updating cumulative traversal metrics from printing progress. There's now an updateCumulativeMetrics function and a printProgress() that only takes a current position
-- printProgress now soles relies on the time since the last progress to decide if it will print or not. No longer uses the number of cycles, since this isn't reliable in the case of nano scheduling
-- GenomeAnalysisEngine now maintains a pointer to the master cumulative metrics. getCumulativeMetrics never returns null, which was handled in some parts of the code but not others.
-- Update all of the traversals to use the new updateCumulativeMetrics, printProgress model
-- Added progress callback to nano scheduler. Every bufferSize elements this callback is invoked, allowing us to smoothly update the progress meter in the NanoScheduler
-- Rename MapFunction to NanoSchedulerMap and the same for reduce.
-- Refactored TraverseLoci into old linear version and nano scheduling version
-- Temp. GATK argument to say how many nano threads to use
-- Can efficiently scale to 3 threads before blocking on input
-- Instead of returning directly the result of map(), returns a MapResult object with the value and a reduceMe flag.
-- Reduce function respects the reduceMe flag
-- Code cleanup and more documentation
-- Helpful for understanding where the time goes to each bit of the code.
-- Controlled by a local static boolean, to avoid the potential overhead in general
-- TraverseReadsNano prints progress at the end of each traversal unit
-- Fix bugs in TraversalEngine printProgress
-- Synchronize the method so we don't get multiple logged outputs when two or more HMSs call printProgress before initialization at the start!
-- Fix the logic for mustPrint, which actually had the logic of mustNotPrint. Now we see the done log line that was always supposed to be there
-- Fix output formatting, as the done() line was incorrectly shifting over the % complete by 1 char as 100.0% didn't fit in %4.1f
-- Add clearer doc on -PF argument so that people know that the performance log can be generated to standard out if one wants
- VariantAnnotatorEngine changed to call genotype annotations even if pilups and allele -> likelihood mappings are not present. Current genotype annotations altered to check for null pilupes and null mappings.
-- In the process uncovered two strange things
1 -- qualityScoreByFullCovariateKey was created but never used. Seems like a cache?
2 -- Discovered nasty bug in BaseRecalibrator: https://jira.broadinstitute.org/browse/GSA-534
-- These are like read filters but can be applied either on input, on output, of handled by the walker
-- Previous example of BAQ now uses the general framework
-- Resulted in massive conceptual cleanup of SAMDataSource and ReadProperties! Yeah!
-- BQSR now uses this framework. We can now do BQSR on input, on output, or within a walker
-- PrintReads now handles all read transformers in the walker in map, enabling us to parallelize PrintReads with BAQ and BQSR
-- Currently BQSR is excepting in parallel, which subsequent commit with fix
-- Removed global variable setting in GenomeAnalysisEngine for BAQ, as command line parameters are cleanly handled by ReadTransformer infrastructure
-- In principle ReadFilters are just a special kind of ReadTransformer, but this refactoring is larger than I can do. It's a JIRA entry
-- Many files touched simply due to the refactoring and renaming of classes
-- A higher level interface to declare parallelism capability of a walker. This interface means that the walker can be multi-threaded, but doesn't necessarily support TreeReducible interface, which forces you to have a combine ReduceType operation that isn't appropriate for parallel read walkers
-- Updated ReadWalkers to implement ThreadSafeMapReduce not TreeReducible
-- TraverseReadsNano modified to read in all input data before invoking maps, so the input to TraverseReadsNano is a MapData object holding the sam record, the ref context, and the refmetadatatracker.
-- Update ValidateRODForReads to be tree reducible, using synchronized map and explicitly sort the output map from locations -> counts in onTraversalDone
-- Expanded integration tests to test nt 1, 2, 4.
-- Yes, GenomeLoc.compareTo was broken. The compareTo function only considered the contig and start position, but not the stop, when comparing genome locs.
-- Updated GenomeLoc.compareTo function to account for stop. Updated GATK code where necessary to fix resulting problems that depended on this.
-- Added unit tests to ensure that hashcode, equals, and compareTo are all correct for GenomeLocs
In addition, fix for GSA-310. If supplied -rf argument does not match a known read filter, the list of read filters will be printed, and users directed to the documentation for more information.
-- Previous behavior was unnecessary and causes all sorts of problems with RODs for reads. The old implementation simply failed in this case. The new code handles this correctly by forcing shards to have all of their data on a single contig.
-- Added a PrintReads integration test to ensure this behavior is correct
-- Adding test BAMs that have < 200 reads and span across contig boundaries
-- shardSpan is only calculated when there some ROD is live in the GATK. No sense in paying the cost per read when you don't need it
-- Update contract to allow null span or unmapped span (good catch unittests!)
-- Deleted ReadMetaDataTracker
-- Added function to ReadShard to give us the span from the left most position of the reads in the shard to the right most, which is needed for the new view
-- ReadMetaDataTracker is dead! Long live the RefMetaDataTracker. Read walkers will soon just take RefMetaDataTracker objects. In this commit they take a class that trivially extends them
-- Rewrote ReadBasedReferenceOrderedView to produce RefMetaDataTrackers not the old class.
-- This new implementation produces thread-safe objects (i.e., holds no points to shared state). Suitable for use (to be tested) with nano scheduling
-- Simplified interfaces to use the simplest data structures (PeekableIterator) not the LocusAwareSeekableIterator, since I both hate those classes and this is on the long term trajectory to remove those from the GATK entirely.
-- Massively expanded DataProvider unit tests for ReadBasedReferenceOrderedView
-- Note that the old implementation of offset -> ROD in ReadRefMetaDataTracker was broken for any read not completely matching the reference. Rather than provide broken code the ReadMetaDataTracker only provides a "bag of RODs" interface. If you want to work with the relationship between the read and the RODs in your tool you need to manage the CIGAR element itself.
-- This commit breaks the new read walker BQSR, but Ryan knows this is coming
-- Subsequent commit will be retiring / fixing ValidateRODForReads
Mark DePristo
Yossi Farjoun
Eric Banks
Christopher Hartl
Ryan Poplin