6a639c8ffc
-- Instead of doing a full SW alignment against the reference we read off bubbles from the assembly graph. -- Smith-Waterman is run only on the base composition of the bubbles which drastically reduces runtime. -- Refactoring graph functions into a new DeBruijnAssemblyGraph class. -- Bug fix in path.getBases(). -- Adding validation code to the assembly engine. -- Renaming SimpleDeBruijnAssembler to match the naming of the new Assembly graph class. -- Adding bug fixes, docs and unit tests for DeBruijnAssemblyGraph and KBestPaths classes. -- Added ability to ignore bubbles that are too divergent from the reference -- Max kmer can't be bigger than the extension size. -- Reverse the order that we create the assembly graphs so that the bigger kmers are used first. -- New algorithm for determining unassembled insertions based on the bubble traversal instead of the full SW alignment. -- Don't need the full read span reference loc for anything any more now that we clip down to the extended loc for both assembly and likelihood evaluation. -- Updating HaplotypeCaller and BiasedDownsampling integration tests. -- Rebased everything into one commit as requested by Eric -- improvements to the bubble traversal are coming as a separate push |
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