odgi v0.8.0 - Nascondino

Buildable Source Tarball: odgi-v0.8.0.tar.gz

We introduce a new tool, odgi priv, that allows us to project differentially private synthetic pangenome graphs out of any input. We developed an initial study of differentially private pangenome graphs. Other major updates include improvement to path guided SGD sorting and layout of the graph, and enhancements to odgi extract that avoid subpath fragmentation.

This introduces (in reverse chronological order):

• Clean interface to dropping and keeping paths in odgi paths #450 by ekg
• Use log1p to avoid singularities in odgi priv #449 by ekg
• Implementation of privvg differential privacy sampling algorithm in odgi priv plus documentation and manpage #448 by ekg
• Dramatic improvement in odgi layout performance by avoiding a coordination variable bottleneck #446 by nsmlzl
• Incredible performance boost to odgi sort by avoiding a coordination variable bottleneck #445 by nsmlzl
• Properly manage full range extraction in odgi extract #443 by AndreaGuarracino
• Compressed mode visualization (path depth heatmap) in odgi viz #438 by subwaystation
• Resolve lingering issues with path manipulation that caused graph corruption via odgi flip (outstanding issue: resolve these coordination problems and allow dynamic removal of paths) #436 by ekg
• Improve subpath extraction in odgi extract #435 by AndreaGuarracino
• Print the number of steps in odgi stats #434 by subwaystation
• Actually use the jaccard metric in odgi untangle #432 by ekg
• Get the depth of graph tips in odgi depth #431 by ekg
• Add BED annotation on top of 2D layout in odgi draw (like gfaestus) #429 by AndreaGuarracino
• Avoid making enormous PNGs in odgi draw #422 by AndreaGuarracino
• Error out if odgi untangle has no input cut points when an input set is given #421 by AndreaGuarracino
• Attempt to resolve path fragmentation in odgi extract #419 by AndreaGuarracino
• Allow direct optimization of the graph in odgi sort #418 by AndreaGuarracino
• odgi stats add weighted_feedback_arc and weighted_reversing_join metrics #417 by AndreaGuarracino
• removed unused code from odgi layout #416 by AndreaGuarracino
• Correct default value for path-sgd-iter-max flag of odgi layout subcommand #413 by nsmlzl
• odgi paths: reduce the key space of the ska::flat_hash_map #412 by AndreaGuarracino
• CPANG22: odgi squeeze: manage edge strandness to avoid graph corruption #411 by AndreaGuarracino