-- 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
-- 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.
-- Confirmed that reads spanning off the end of the chromosome don't cause an exception by adding integration test for a single read that starts 7 bases from the end of chromosome 1 and spans 90 bases or so off. Added pileup integration test to ensure this behavior continues to work
-- 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
Eric Banks
Christopher Hartl
Mark DePristo
Yossi Farjoun
Ryan Poplin