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