ebe2edbef3
Problem: -------- PairHMM was generating positive likelihoods (even after the re-work of the model) Solution: --------- The caching idices were never re-initializing the initial conditions in the first position of the deletion matrix. Also the match matrix was being wrongly initialized (there is not necessarily a match in the first position). This commit fixes both issues on both the Logless and the Log10 versions of the PairHMM. Summarized Changes: ------------------ * Redesign the matrices to have only 1 col/row of padding instead of 2. * PairHMM class now owns the caching of the haplotype (keeps track of last haplotypes, and decides where the caching should start) * Initial condition (in the deletionMatrix) is now updated every time the haplotypes differ in length (this was wrong in the previous version) * Adjust the prior and probability matrices to be one based (logless) * Update Log10PairHMM to work with prior and probability matrices as well * Move prior and probability matrices to parent class * Move and rename padded lengths to parent class to simplify interface and prevent off by one errors in new implementations * Simple cleanup of PairHMMUnitTest class for a little speedup * Updated HC and UG integration test MD5's because of the new initialization (without enforcing match on first base). * Create static indices for the transition probabilities (for better readability) [fixes #47399227] |
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| .. | ||
| genotyper | ||
| nanoScheduler | ||
| pairhmm | ||
| recalibration | ||
| ContigComparatorUnitTest.java | ||
| SWPairwiseAlignmentUnitTest.java | ||