v0.9.3

Buildable Source Tarball: odgi-v0.9.3.tar.gz

What's Changed

• Add header to output for sample counts in stats command by @AndreaGuarracino in #608
• added checks for apple sillicon and cmake4.0+ version by @hlakshmidevi10 in #612
• odgi similarity: a bit more parallelization for deep graphs by @AndreaGuarracino in #614

New Contributors

• @hlakshmidevi10 made their first contribution in #612

Full Changelog: v0.9.2...v0.9.3

v0.9.2

Buildable Source Tarball: odgi-v0.9.2.tar.gz

What's Changed

• odgi similarity: Add option to emit all pairs of paths/groups in similarity computation by @AndreaGuarracino in #605

Full Changelog: v0.9.1...v0.9.2

v0.9.1

Buildable Source Tarball: odgi-v0.9.1.tar.gz

What's Changed

• [Feature] Enable GPU to accelerate odgi-layout with massive speedup. Build with a flag USE_GPU by @tonyjie in #593
• Update README.md by @Overcraft90 in #594
• Update README.md by @Overcraft90 in #595
• odgi similarity masked by @AndreaGuarracino in #600
• consider the mask when filling bp_length by @AndreaGuarracino in #601
• update GitHub Actions workflow to use ubuntu-latest by @AndreaGuarracino in #602

New Contributors

• @Overcraft90 made their first contribution in #594

Full Changelog: v0.9.0...v0.9.1

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