-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.
- Merged Roger's metrics with Mauricio's optimizations
- Added Stats for DiagnoseTargets
- now has functions to find the median depth, and upper/lower quartile
- the REF_N callable status is implemented
- The walker now runs efficiently
- Diagnose Targets accepts overlapping intervals
- Diagnose Targets now checks for bad mates
- The read mates are checked in a memory efficient manner
- The statistics thresholds have been consolidated and moved outside of the statistics classes and into the walker.
- Fixed some bugs
- Removed rod binding
Added more Unit tests
- Test callable statuses on the locus level
- Test bad mates
- Changed NO_COVERAGE -> COVERAGE_GAPS to avoid confusion
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
* Fixed output format to get a valid vcf
* Optimzed the per sample pileup routine O(n^2) => O(n) pileup for samples
* Added support to overlapping intervals
* Removed expand target functionality (for now)
* Removed total depth (pointless metric)
Infrastructure:
* Added static interface to all different clipping algorithms of low quality tail clipping
* Added reverse direction pileup element event lookup (indels) to the PileupElement and LocusIteratorByState
* Complete refactor of the KeyManager. Much cleaner implementation that handles keys with no optional covariates (necessary for on-the-fly recalibration)
* EventType is now an independent enum with added capabilities. All functionality is now centralized.
BQSR and RecalibrateBases:
* On-the-fly recalibration is now generic and uses the same bit set structure as BQSR for a reduced memory footprint
* Refactored the object creation to take advantage of the compact key structure
* Replaced nested hash maps with single hash maps indexed by bitsets
* Eliminated low quality tails from the context covariate (using ReadClipper's write N's algorithm).
* Excluded contexts with N's from the output file.
* Fixed cycle covariate for discrete platforms (need to check flow cycle platforms now!)
* Redfined error for indels to look at the previous base in negative strand reads (using new PE functionality)
* Added the covariate ID (for optional covariates) to the output for disambiguation purposes
* Refactored CovariateKeySet -- eventType functionality is now handled by the EventType enum.
* Reduced memory usage of the BQSR script to 4
Tests:
* Refactored BQSRKeyManagerUnitTest to handle the new implementation of the key manager
* Added tests for keys without optional covariates
* Added tests for on-the-fly recalibration (but more tests are necessary)
* added support to base before deletion in the pileup
* refactored covariates to operate on mismatches, insertions and deletions at the same time
* all code is in private so original BQSR is still working as usual in public
* outputs a molten CSV with mismatches, insertions and deletions, time to play!
* barely tested, passes my very simple tests... haven't tested edge cases.
Eric reported this bug due to the reduced reads failing with an index out of bounds on what we thought was a deletion, but turned out to be a read starting with insertion.
* Refactored PileupElement to distinguish clearly between deletions and read starting with insertion
* Modified ExtendedEventPileup to correctly distinguish elements with deletion when creating new pileups
* Refactored most of the lazyLoadNextAlignment() function of the LocusIteratorByState for clarity and to create clear separation between what is a pileup with a deletion and what's not one. Got rid of many useless if statements.
* Changed the way LocusIteratorByState creates extended event pileups to differentiate between insertions in the beginning of the read and deletions.
* Every deletion now has an offset (start of the event)
* Fixed bug when LocusITeratorByState found a read starting with insertion that happened to be a reduced read.
* Separated the definitions of deletion/insertion (in the beginning of the read) in all UG annotations (and the annotator engine).
* Pileup depth of coverage for a deleted base will now return the average coverage around the deletion.
* Indel ReadPositionRankSum test now uses the deletion true offset from the read, changed all appropriate md5's
* The extra pileup elements now properly read by the Indel mode of the UG made any subsequent call have a different random number and therefore all RankSum tests have slightly different values (in the 10^-3 range). Updated all appropriate md5s after extremely careful inspection -- Thanks Ryan!
phew!
The GATK engine will now provide a GATKSAMRecord to all tools which incorporates the functionality used by the GATK to the bam file (ReadGroups, Reduced Reads, ...).
* No tools should create SAMRecord anymore, use GATKSAMRecord instead *
-- Supports ReadBackedPileup -> FragmentCollection as before
-- Added support for List<SAMRecord> -> FragmentCollection for Ryan's haplotype caller
-- General cleanup, renaming, move to separate package, more extensive unit tests, etc.
-- Added toFragment() function to ReadBackedPileup interface
-- removed intermiate functions. Now only original version and best optimized new version remain
-- Moved general artificial read backed pileup creation code into ArtificialSamUtils
-- Uses mayOverlapRoutine in ReadUtils
-- Attempts to be smart when doing overlap calculation, to avoid unnecessary allocations
-- PileupElement now comparable (sorts on offset than on start)
-- Caliper microbenchmark to assess performance
-- UnitTests for key functions on reduced reads
-- PileupElement calls static functions in ReadUtils
-- Simple routine that takes a reduced read and fills in its quals with its reduced qual
David Roazen
Eric Banks
Roger Zurawicki
Mauricio Carneiro
Ryan Poplin
Guillermo del Angel
Mark DePristo