v1.5.3

Bug Fixes

Origin-spanning features on circular assemblies

A feature that runs across the origin of a circular assembly is stored with its start position after its end position. Nothing downstream expected that, so a single wrapping feature could stop a project outright.

• Curation no longer crashes on a wrapping feature. Every boundary adjustment handed those coordinates straight to a sequence-extraction call that refuses a start after an end, so the whole curation step exited with an error and the run stopped. Sequence extraction and length are now wrap-aware, and extension or trimming may cross the origin on a circular contig. Linear assemblies behave exactly as before.
• Export writes a wrapping feature as two intervals in the submission table. A single line spanning the origin does not mean "wraps" to table2asn, it means "minus strand", so the feature was being submitted backwards. Also fixed in export: the 3' end of a transl_except, minus-strand exon coordinates in the GFF, and a crash in the PCG outlier review when an exon wrapped.
• Validation checks are circular-aware. Overlap, containment, and length tests measured a wrapping feature as if it ran the long way around the genome, so genuine overlaps went unreported and non-overlapping features were flagged.
• The control region keeps its extension when a neighbour wraps. An origin-adjacent OH call is now bounded by the wrapping feature rather than by the contig edge. Three test samples were finishing with a stunted control region and a spurious "below minimum length" warning.
• The annotation editor handles wrapping throughout: nudging boundaries, copy FASTA, rRNA alignment, the boundary viewer, the zoom track, the linearize guard, and merge / un-merge.
• Rotating an assembly now warns when the requested start gene is not present, and when the new origin would cut through a feature.
• MITOS2 annotations use the right contig length. On a multi-contig unit the first contig's length was applied to every contig, which mis-placed wrap calculations on all the others.

Database writes

• Scaffold mappings could be wiped. The delete and insert halves of a scaffold-mapping update were sent as two independent database operators with no guaranteed ordering, so the delete could land last and leave the table empty. Both now run inside a single transaction from the pipeline driver.

HPC

• NOAA SEDNA memory now scales with the retry attempt, matching every other cluster profile. A retry was re-requesting the same memory that had just failed, so a step that ran out of memory would fail again identically.

Container builds

• A stale package archive can no longer be shipped in the image. The Dockerfile picks up the package archive by name order, so a leftover build of an older version won out over the new one and the container quietly shipped the wrong MitoPilot. All three deploy scripts now clear old archives first.

Documentation

• The website has been rewritten and reorganized: Get Started is now a full tutorial built around the bundled test project, the README is a landing page with installation moved to its own article, and the curation documentation is clade-neutral with the ruleset chosen in the app rather than hand-written.
• The article on handling difficult assemblies replaces the old multiple-assemblies page, the reference index is grouped by topic, screenshots are regenerated for the current app, and a citation file is included with the package.
• A maintainer guide for building the container was added, and the legacy GenBank download script was retired.

Note
To update older MitoPilot projects, please run MitoPilot::backwards_compatibility(). This will add any missing fields to the SQL database and attempt to update the Docker/Singularity container version in your project .config file.

Full Changelog: 1.5.2...1.5.3