3671e41b0c
A new PairHMM implementation for read/haplotype likelihood calculations. Output is the same as the LOGLESS_CACHING version. Instead of allocating an entire (read x haplotype) matrix for each HMM state, this version stores sub-computations in 1D arrays. It also accesses intersections of the (read x haplotype) alignment in a different order, proceeding over "diagonals" if we think of the alignment as a matrix. This implementation makes use of haplotype caching. Because arrays are overwritten, it has to explicitly store mid-process information. Knowing where to capture this info requires us to look ahead at the subsequent haplotype to be analyzed. This necessitated a signature change in the primary method for all pairHMM implementations. We also had to adjust the classes that employ the pairHMM: LikelihoodCalculationEngine (used by HaplotypeCaller) PairHMMIndelErrorModel (used by indel genotyping classes) Made the array version the default in the HaplotypeCaller and the UnifiedArgumentCollection. The latter affects classes: ErrorModel GeneralPloidyIndelGenotypeLikelihoodsCalculationModel IndelGenotypeLikelihoodsCalculationModel ... all of which use the pairHMM via PairHMMIndelErrorModel |
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| .. | ||
| genotyper | ||
| gvcf | ||
| haplotype | ||
| haplotypeBAMWriter | ||
| nanoScheduler | ||
| pairhmm | ||
| recalibration | ||
| smithwaterman | ||
| ContigComparatorUnitTest.java | ||