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rchikhi committed Nov 20, 2017
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* Time and memory optimisations :

* Faster k-mer counting (inspired by KMC3)
* Faster k-mer counting (inspired by KMC3 but not yet as fast :)

* More efficient graph representation using compressed vectors (in `GraphUnitigs.cpp`)

* Faster unitigs compaction algorithm (improvements in BCALM engineering)
* Faster unitigs compaction (engineering improvements in BCALM code)

* New compact encoding scheme to load the abundance values in memory (encoded on 8 bits, value range = 0 to 50k with 5% max error)


* Parameterizable graph simplifications steps (see `Graph.hpp`)

* Parameterizable graph simplifications steps (see `Graph.hpp` and Minia): optional tip-clipping, bulge removal, erroneous connection

* Preliminary support for loading unitigs (in `GraphUnitigs.cpp`) from a GFA1 graph format generated by BCALM (using `scripts/convertToGFA.py` in BCALM repository)

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