🛠️ Minor Release

This minor release main change is the subsitution of GeneMarkS-T for TransDecoder2 to predict ORFs. This change was done due to the outdating of GMST and its constant issues that we could not solve. Moreover, some essential bugfixes and QOL improvements have been added to the repository. Read below for more information.

✨ Improvements

• Automatic detection of @SQ headers in SAM files.
• Added multiple checks for gene_name attributes in reference annotations when required.
• Improved error handling in rescue rules when no valid rules are provided.
• Significantly faster rescue file writing (no shell call overhead).
• Enhanced output management and reduced type errors in filterML.

🐞 Bugfixes

• Fixed logging: missing files now raise appropriate warnings or errors.
• Boolean values in the config file are now correctly detected by the wrapper.
• IsoAnnotLite now checks for the gene_name attribute in the reference.
• Fixed rescue output generation when no GTF is provided.
• Custom TP/TN sets and remove_columns in filterML are now handled correctly.
• SQANTI-reads adapted to the updated argument parser.
• Fixed string conversion issue in myQueryTranscripts.__str__() when printing None.
• TSS ratio counts have been corrected.
• CDS prediction bugs fixed.
• Fixed IO handling and logging behaviors.

🔧 Changes

• GMST has been replaced by TD2.
• SQANTI-reads updated to use the new argument format.
• Output filenames for CDS predictions have been made more descriptive.
• Examples updated for consistency with the new version.
• Rescue script reverted to its previous argument style.

📌 What's Changed (from PRs)

• Fix failure of myQueryTranscripts.__str__() when printing value of an invalid object [#455] by @diekhans
• TSS ratio counts fixed [#457](#457) by @pabloati
• IO handling and logging improved [#462] by @pabloati
• Rescue argparse fixes [#463] by @pabloati
• Fixed custom TP/TN sets and remove_columns [#465]by @FabianJetzinger
• Included SAM header detection [#468] by @pabloati
• Added user input validation on ´IsoAnnotLite´ and ´gene_name´ [#469] by @pabloati
• CDS prediction fixes [#470] by @pabloati
• Improved output management [#477] by @pabloati
• Type error fixes in filters [#478] by @pabloati
• ORF prediction enhancements [#486] by @pabloati
• Updated filter testing suite [#487] by @pabloati
• Version bump to v5.5 [#490] by @pabloati
• Small update to SQANTI-reads to standarize the format of the GTFs [#494] by @TianYuan-Liu
• Fix to SQANTI filter rules, to apply multioptions in categies as OR, rather than AND [#497] by @FabianJetzinger

🙌 New Contributor

• @FabianJetzinger made their first contribution in [#465](#465) 🎉

🔗 Full Changelog: v5.4...v5.5