v0.9.0

Buildable Source Tarball: odgi-v0.9.0.tar.gz

What's Changed

• odgi draw: put labels on top of everything in the SVG output by @AndreaGuarracino in #571
• odgi viz: longer path names by default; odgi positions: emit all positions by @AndreaGuarracino in #573
• odgi stats: -S per default by @subwaystation in #578
• Include STL so steps_of_handle works by @dpryan79 in #582
• fix variable type to avoid wrong lengths in the untangled PAF by @AndreaGuarracino in #583
• odgi flip -r/--ref-flips: flip with respect to a set of paths (used as references) by @AndreaGuarracino in #585
• check the GFA while reading it by @AndreaGuarracino in #591

New Contributors

• @dpryan79 made their first contribution in #582

Full Changelog: v0.8.6...v0.9.0

v0.8.6

Buildable Source Tarball: odgi-v0.8.6.tar.gz

What's Changed

• fix bug to avoid underflows in odgi viz by @AndreaGuarracino in #570

Full Changelog: v0.8.5...v0.8.6

v0.8.5

Buildable Source Tarball: odgi-v0.8.5.tar.gz

What's Changed

• odgi stats: deactivate 1D layout metrics in MultiQC mode by @subwaystation in #544
• Tutorial: Sort and layout power ups. by @subwaystation in #552
• update version of checkout in ci by @kojix2 in #554
• odgi draw: fix SVG output by @AndreaGuarracino in #555
• write highlights over the rasterized image by @ekg in #547
• write highlights over black/grey lines in SVG by @AndreaGuarracino in #556
• odgi draw: add labels in the SVG output by @AndreaGuarracino in #557
• odgi extract: avoid duplicated subpaths by @AndreaGuarracino in #559
• odgi draw: add node sparsification factor for SVG output by @AndreaGuarracino in #558
• odgi paths ... --non-reference-ranges: emit last non-ref path range, if any by @AndreaGuarracino in #564
• Upgrade pybind11 to current head by @JervenBolleman in #566
• fix outgoing links of the last node by @AndreaGuarracino in #568
• add uncalled bases to non-ref-nodes by @AndreaGuarracino in #569
• odgi paths: private/core/accessory sequence classification by @AndreaGuarracino in #565

Full Changelog: v0.8.4...v0.8.5

v0.8.4

Buildable Source Tarball: odgi-v0.8.4.tar.gz

What's Changed

• add conda-forge to conda installation instructions by @aryarm in #500
• fix odgi untangle PAF output bug by @AndreaGuarracino in #501
• fix ODGI for GCC 13.1 by @subwaystation in #507
• Less verbose logging by @AndreaGuarracino in #508
• odgi heaps: avoid missing groups by @AndreaGuarracino in #509
• Fix applying_ordering by @AndreaGuarracino in #510
• Add missing library by @kojix2 in #512
• heaps: plot down to 0 on the y-axis by @subwaystation in #514
• Progress in odgi pav by @AndreaGuarracino in #517
• Avoid out of bound (segfault) in odgi similarity by @AndreaGuarracino in #520
• odgi extract refresh: add -O/--optimize option and put -d by default by @AndreaGuarracino in #522
• odgi paths: show non-reference nodes and path/step ranges by @AndreaGuarracino in #523
• odgi extract: check there are no duplicated path ranges by @AndreaGuarracino in #525
• odgi extract: a bit more aggressive subpath merging by default by @AndreaGuarracino in #528
• odgi extract: manage input path range boundaries by @AndreaGuarracino in #531
• odgi paths -H on subgraphs by @AndreaGuarracino in #534
• Nix building by @ekg in #535
• depth: option to use unique window depths by @kdm9 in #538
• make svg drawing work with colors by @ekg in #539
• odgi paths ... --non-reference-nodes: emit also node length by @AndreaGuarracino in #541

New Contributors

• @aryarm made their first contribution in #500
• @kojix2 made their first contribution in #512
• @kdm9 made their first contribution in #538

Full Changelog: v0.8.3...v0.8.4

odgi 0.8.3 - Manutenuto

Buildable Source Tarball: odgi-v0.8.3.tar.gz

This release introduces a new command, odgi similarity, to compute the similarity (or dissimilarity) between paths or groups of paths. Moreover, it fixes and optimizes several commands. Importantly, now it is possible to compile odgi with Clang, on macOS and on ARM!

This introduces:

• ensure that the optimal sum_of_path_node_distances is actually 1 #466 by @subwaystation
• add yaml output for -j -w when all paths are emitted #467 by @subwaystation
• odgi stepindex: unsampled step index #468 by @AndreaGuarracino
• odgi untangle: verbose log #469 by @AndreaGuarracino
• odgi tension: set the distance to 0 after each step instead of each path #470 by @tonyjie
• fix the iteration bound: now the iter_max we set is the exact running iteration #471 by @tonyjie
• script to generate release binaries #472 by @subwaystation
• fix smoothxg-offending import #473 by @AndreaGuarracino
• odgi inject: use a key that is really unique across annotations #476 by @AndreaGuarracino
• Optimization of zeta preprocessing #480 by @nsmlzl
• Fix versioning #482 by @AndreaGuarracino
• odgi paths: initialize vector values #483 by @AndreaGuarracino
• odgi flip: avoid introducing useless edges and losing edges from the original graph #485 by @AndreaGuarracino
• odgi paths allows a specific occurrence of the delimiter #488 by @AndreaGuarracino
• fix a bug with reference-guided PG-SGD #490 by @subwaystation
• odgi overlap: fix header #492 by @AndreaGuarracino
• Portability fixes to build with Clang, on macOS, and on ARM #494 by @sampsyo
• New odgi similarity command #498 by @AndreaGuarracino

odgi 0.8.2 - Biccino

Buildable Source Tarball: odgi-v0.8.2.tar.gz

This introduces:

• always emit long version format #456 by @AndreaGuarracino
• optionally scale haplotype matrix cells by node length #457 by @ekg
• increment progress-meter of odgi sort less frequently #458 by @nsmlzl
• increment progress-meter of odgi layout less frequent #459, #462 by @AndreaGuarracino @nsmlzl
• odgi extract: avoid creating subgraphs with empty subpaths #460 by @AndreaGuarracino
• odgi prune: remove empty paths #460 by @AndreaGuarracino

odgi 0.8.1 - Piccino

Buildable Source Tarball: odgi-v0.8.1.tar.gz

This introduces:

• non-binary haplotype matrix #452 by @ekg
• typos and tweak in odgi flip by 98c139e @AndreaGuarracino

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

odgi 0.7.3 - Fissaggio

Buildable Source Tarball: odgi-v0.7.3.tar.gz

This introduces:

• fixed (and optimized) odgi flip, avoiding path metadata corruption (#410);
• fixed odgi squeeze, that now manages edge stradness correctly;
• fixed odgi paths's out-of-memory problem (#412);
• documentation cleaning (#413)
• odgi layout cleaning (#416)
• odgi sort allow users only to optimize the graph, and not sort it (#418);
• added in odgi stats new sorting-goodness metrics (#417);
• odgi extract was a bit optimized and now it allows users to merge close subpaths to avoid fragmented subgraphs (#419);
• odgi untangle emits an error if there are no cut points in input (#421);
• odgi draw avoid too big images that would require too much memory (#422);

odgi 0.7.2 - Radler

Buildable Source Tarball: odgi-v0.7.2.tar.gz

This lemon beer release comes with lot's of new features and some bug fixes:

• Fixed libbf compilation issue.
• The stepindex throws an error if it was fed an empty path.
• xp index: Delete all temporary files after index generation.
• More stringent node identifier validation when parsing from GFA.
• odgi groom: Added a reference-based mode.
• odgi sort: rPG-SGD allows to globally sort by given references.
• odgi untangle: We can select gene order groups for plotting with gggenes.
• New subcommand odgi procbed: Pprocrustes-BED: Intersect and adjust BED interval into PanSN-defined path subranges. Lift BED files into graphs produced by odgi extract. Uses path range information in the path names.
• New subcommand odgi inject: Inject BED interval ranges as paths in the graph.
• New subcommand odgi flip: Flip (reverse complement) paths to match the graph.
• Docs:
  • Sync it with the changes above
  • Added a new tutorial of how to inject gene arrows with odgi untangle.
  • Added a section explaining how to apply the rPG-SGD.

Full Changelog: v0.7.1...v0.7.2