3bfca0ccfd
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) |
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| .. | ||
| ArtificialPatternedSAMIteratorUnitTest.java | ||
| ArtificialSAMFileWriterUnitTest.java | ||
| ArtificialSAMQueryIteratorUnitTest.java | ||
| ArtificialSAMUtilsUnitTest.java | ||
| GATKSAMRecordUnitTest.java | ||
| ReadUtilsUnitTest.java | ||