The GATK -L unmapped is for GenomeLocs with SAMRecord.NO_ALIGNMENT_REFERENCE_NAME, not SAMRecord.getReadUnmappedFlag()
Previously unmapped flag reads in the last bin were being printed while also seeking for the reads without a reference contig.
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.
* new unit tests for the alignment shift properties of reduce reads
* moved unit tests from ReadUtils that were actually testing GATKSAMRecord, not any of the ReadUtils to it.
* cleaned up ReadUtilsUnitTest
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!
* if the adaptor boundary is more than MAXIMUM_ADAPTOR_SIZE bases away from the read, then let's not clip anything and consider the fragment to be undetermined for this read pair.
* updated md5's accordingly
The algorithm wasn't accounting for the case where the read is the reverse strand and the insert size is negative.
* Fixed and rewrote for more clarity (with Ryan, Mark and Eric).
* Restructured the code to handle GATKSAMRecords only
* Cleaned up the other structures and functions around it to minimize clutter and potential for error.
* Added unit tests for all 4 cases of adaptor boundaries.
Khalid Shakir
Mauricio Carneiro
Ryan Poplin
David Roazen