v0.6.0

What's Changed

• Heuristic wfmash by @AndreaGuarracino in #315
• make stats option consistent with help by @mbhall88 in #317
• handle version reporting if pggb is symlinked by @ASLeonard in #318
• check PanSN in the input FASTA by @AndreaGuarracino in #321
• add entire scripts folder in bin by @AndreaGuarracino in #323
• update vg deconstruct to version 1.50.1 by @AndreaGuarracino in #324
• update gfaffix by @AndreaGuarracino in #325
• update MultiQC to v1.15 by @subwaystation in #326
• fix partition-before-pggb -p bug by @subwaystation in #327
• update smoothxg and odgi by @AndreaGuarracino in #330
• update partition-before-pggb by @AndreaGuarracino in #332
• Update wfmash with the new MashMap3 by @AndreaGuarracino in #333
• Update documentation and GitHub workflows by @AndreaGuarracino in #335
• update parameters and error messages by @AndreaGuarracino in #336
• update gffafix by @AndreaGuarracino in #338
• Fix libwfa2cpp in the Docker image by @AndreaGuarracino in #340
• fix parameter parsing by @AndreaGuarracino in #341
• update multiqc and vg by @AndreaGuarracino in #343
• Minimize the minimal pggb command line by @AndreaGuarracino in #346
• update odgi/smoothxg by @AndreaGuarracino in #347
• Mandatory -o/--output-dir, remove --no-pansn and better errors reporting by @AndreaGuarracino in #348
• Fixes in partition-before-pggb by @AndreaGuarracino in #349
• update wfmash by @AndreaGuarracino in #350
• A bit stronger filtering for mappings and matches by @AndreaGuarracino in #351
• fix -n/-c in partition-before-pggb by @AndreaGuarracino in #352
• update wfmash by @AndreaGuarracino in #355
• fix typo in usage regarding --no-splits by @kdm9 in #354
• update re-fixed wfmash by @AndreaGuarracino in #358
• re-re-fix wfmash by @AndreaGuarracino in #359
• update wfmash by @AndreaGuarracino in #361
• update vg and multiqc by @AndreaGuarracino in #362
• allow resuming for only variant calling by @AndreaGuarracino in #365
• stable link for data.table by @AndreaGuarracino in #366
• update smoothxg's SPOA and abPOA by @AndreaGuarracino in #367
• update smoothxg (abPOA) by @AndreaGuarracino in #368
• vg deconstruct 1.40.0 (again) and sort decomposed VCF file by @AndreaGuarracino in #369
• update wfmash/smoothxg/odgi by @AndreaGuarracino in #371
• add option for filenames with param values by @AndreaGuarracino in #372
• multiqc 1.21, bcftools 1.19 by @subwaystation in #376
• update smoothxg by @AndreaGuarracino in #380
• update smoothxg by @subwaystation in #381
• explicit separator for vg 1.40.0 by @AndreaGuarracino in #384
• update wfmash/seqwish/smoothxg/odgi by @AndreaGuarracino in #386
• fix odgi viz underflow by @AndreaGuarracino in #387

New Contributors

• @mbhall88 made their first contribution in #317
• @ASLeonard made their first contribution in #318
• @kdm9 made their first contribution in #354

Full Changelog: v0.5.4...v0.6.0

pggb 0.5.4 - Fatica

The main power-ups in this version are in smoothxg:

• the partial order alignment (POA) is executed on unique sequences by duplicating the POA blocks before their alignment, strongly improving the performance;
• final graphs no longer contain uncovered edges, leading to a bit simpler graph topologies.

Moreover, we update vcfwave in order to correctly manage inversions in the VCF file normalization.

Updating pggb's components, we fixed several bugs and now the log files will be a bit less verbose (in order to avoid gigabyte-scale logs for long runs).

This introduces:

• update smoothxg to perform the POA on unique sequences #280 by @AndreaGuarracino
• fix versioning #282 by @AndreaGuarracino
• support metric parameter suffixes #290 by @ekg
• update singularity syntax in the README.md #293 by @petersudmant
• add tools for gfa2evaluation in Dockerfile #295 by @subwaystation
• update smoothxg to avoid uncovered edges #304 by @AndreaGuarracino
• update pggb's components #281, #283, #285, #286, #296, #303 by @AndreaGuarracino
• Update vcflib to get the fixed vcfwave #311 by @AndreaGuarracino

pggb 0.5.3 - Eseguito

• fix block_length management and tweaks defaults #269 by @AndreaGuarracino
• update odgi to fix an odgi unchop bug by @AndreaGuarracino
• fix partition-before-pggb calling in the Dockerfile #271 #273 by @thomasraulet
• improve compatibility with Nextfllow #272 by @subwaystation
• plot also uncalled bases #274 by @AndreaGuarracino @subwaystation
• executable scripts #275 by @AndreaGuarracino

pggb 0.5.2 - Ciclico

• Emit tools' version in the LOG/YAML output #248 by @AndreaGuarracino
• Remove the smoothxg loop as it has been internalized in it #249, #251 by @AndreaGuarracino, @subwaystation
• Filter alignments with gap-compressed identity below -p x 0.8 #250 by @AndreaGuarracino
• Call variants first (if requested), then compute the statistics and visualizations later (if requested) #254 by @AndreaGuarracino
• Make paf2net more robust by supporting any kind of wfmash's output by @AndreaGuarracino
• Better documentation #260, #261 by @AndreaGuarracino
• Fix the management of mandatory parameters #263 by @AndreaGuarracino
• Optimized build of pggb tools in Docker/Singularity by #265, #264 @AndreaGuarracino
• Updates abpoa and smoothxg to avoid a segmentation fault #266 by @AndreaGuarracino

pggb 0.5.1 - Speranza

This introduces:

• gcc-11 for building the tools in the Docker/Singularity image #240 by @ekg
• a heavily reworked pggb script to improve its maintainability, with minor bug and typos fixes, and improvement in the LOG/YAML outputs #242 by @AndreaGuarracino
• the partition-before-pggb script to perform sequence partitioning before pggb #243 by @AndreaGuarracino
• update for seqwish and its compilation to improve its portability #244 by @AndreaGuarracino
• optional (skippable) graph normalization step #246 by @AndreaGuarracino

pggb 0.5.0 - Bidirezionale

The main change is the introduction of the bidirectional wfλ in wfmash, which allows a full exploration of the high-order alignment matrix without blowing up with the memory. This leads to more and better anchors that tend to simplify the alignments during the patching phase, therefore even improving the runtime for the whole pggb run.

This introduces:

• the --version flag to display the version of pggb #218 by @AndreaGuarracino
• automatically set thread count #220 by @ekg
• docker/singularity: fix versioning, smaller image, update vcflib, and faster building #222 #224 by @AndreaGuarracino
• improved SPOA's portability (for Docker/Singularity and Bioconda) #223 by @AndreaGuarracino
• introduction of BiWFλ, bidirectional flavor of wfλ in wfmash #231 by @AndreaGuarracino
• additional diagnostic viz displaying a vertically summarized view of the graph #233 by @subwaystation
• the unchop of the graph normalized by GFAFfix #237 by @AndreaGuarracino
• all tools were updated (in particular, improved wfmash and faster odgi sort and layout) #230 #234 #235 #236

Shareable

Point release with updates to wfmash and a change to the segment length default (now 5k).

pggb 0.4.0 - Pasticcino

This introduces:

• temporary directory management (#197);
• improvements of the alignments (#195, #198);
• samtools, fastix, igraph, pycairo, and pafplot in the docker/singularity image (#204);
• better management of the -r/--resume flag (#205);
• great improvement in graph normalization by replacing abPOA with SPOA, running it in local mode (#207). This resolves the SNV arrays introduced during the smoothing;
• abPOA/SPOA selection (#209);
• variant decomposition with vcfbub and vcfwave (#211)

pggb 0.3.1 - Pasticcione

This:

• updates in how tools are compiled/built to ensure greater inter-system compatibility;
• handles -n differences between pggb and wfmash;
• outputs only one final graph with final suffix.

pggb 0.3.0 - Esplorazione

This introduces major changes in pggb's' interface and alignment step for supporting high-divergence genomes and compressed graph representations:

• new wfmash version for aligning highly divergent sequences;
• new default values;
• simpler interface, with a few changes:
  • drop -U/--normalize, -I/--block-id-min, and -M/--no-merge-segments
  • merge -v and -L in -v/--skip-viz )
  • replace -F with -M for requesting the MAF output;
• make 1D and 2D visualizations by default (-v/--skip-viz for disabling this);
• mandatory normalization with GFAFfix;
• do not keep intermediate files by default (-A to keep them);
• updated seqwish, smoothxg, odgi, gffafix, vg;
• new (still WIP) documentation at https://pggb.readthedocs.io/, with tutorials for PanSN-spec naming and sequence clustering;
• addded bcftools statistics in the MultiQC report;
• added PAF file format input (-a/--input-paf) to skip the alignment step;
• emit 2D graph layouts in TSV too for visualizing them with gfaestus;
• timer for gffafix execution;
• use bgzip for compressing VCF files;