Harun Mustafa

Seeding and chaining optimizations

1

- [x] Filter out low complexity seeds using sdust - [x] Optimize chainer: reduce memory overhead - [x] AVX2 instructions in chainer - [x] Simplify labeled seeding - [x] Unit...

This format reports the node IDs of alignment paths. See ["The Graph Alignment Format (GAF)"](https://github.com/lh3/gfatools/blob/master/doc/rGFA.md#the-graph-alignment-format-gaf) and ["Sequence Alignment/Map Optional Fields Specification"](https://samtools.github.io/hts-specs/SAMtags.pdf)

- No default limit on the total number of output alignments - If a seed has a filtered-out label, report the seed as an alignment without extending it - Annotate...

This delegates builder destruction to the std::vector. This reverses the order in which builders are written to disk, so I'm not sure if this breaks anything. The tests seem to...

This adds: - Statistical significance tests for differential assembly using binary and count annotations - The ability to stream annotation column counts from disk - Addition of a disk-streaming row-major...

possibility to adapt builders for partitions with single elements

5

As part of unit testing, I've been creating hash tables with very few keys (e.g., making a sshash dictionary for a sequence set with a single super k-mer), frequently triggering...

Currently this is only implemented for SSHash graphs. This change stores a bit vector that indicates the breakpoints for monochromatic unitigs in the SSHash graph. This allows us to maintain...

Support a coordinate-to-accession map to a graph, mapping an annotation label+coordinate to an accession

1

For now, this is implemented as a graph extension, but the ideal thing would be to have a wrapper for MultiLabelAnnotation.