Pattern Search on Sequence Data #167
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Taepper
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src/silo/storage/sequence_store.cpp
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| const auto* negated_reference_bitmap = | ||
| this->getBitmap(genome_pos, this->reference_genome[genome_pos]); | ||
| const auto* n_symbol_bitmap = this->getBitmap(genome_pos, NUCLEOTIDE_SYMBOL::N); | ||
| auto pure_mutation = std::make_unique<roaring::Roaring>(roaring_bitmap_andnot( | ||
| &negated_reference_bitmap->roaring, &n_symbol_bitmap->roaring | ||
| )); |
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@Taepper I did not find where the reference genome bitmap gets flipped. Does SILO still do it? Anyways, this part is not yet correct. Should we do a union over all bitmaps except the reference bitmap to get the ones that are actually mutated to a symbol other than N
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Oh, it should definitely still happen! For now you can do that, but the bitmap flipping must have gotten lost in refactoring somewhere .. it will be reenabled. But yes, you can Save those bitmaps. I guess "mutated to other than - or N" in order to not need a workaround for that anymore!
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Preparation of pattern search #165!
Most relevant parts of the edits should happen in the TODO marked areas. Of course, the additional data structures that need to be added in the sequence store which are not yet added, will make up a large part of this PR