Changelog

0.3

• Add liftover troubleshooting and shared resource-script documentation.
• Add blacklist and CGI CrossMap/UCSC liftOver overlap comparisons for hg19 and mm10, including unmerged, merge -d 100, and merge -d 200 results.
• Report both native-truth recall and liftover prediction-side PPV, with confidence warnings for fragmented and low-recovery mappings.
• Improve FeatureBED, GeneBED, deduplication, CLI, configuration, and resource documentation.

0.2.0

• Ensure packaged BED resources are sorted by chromosome, start, and end.
• Sort generated GeneBED, FeatureBED, TSS/TES, deduplicated, CGI, and blacklist outputs regardless of the selected interval-writing backend.
• Add coverage for sorted interval generation and packaged BED validation.
• Complete existing RC files with missing commented settings and normalize commented variables to the #SJCAB_... form.
• Add aligned component-aware list output with a source column.
• Store installed GeneBEDs under genebed/ instead of bed/.
• Record installed FeatureBED source GTF filenames in installed.tsv and show them in list feature.

0.1.9

• See the release history in the repository for the preceding configuration, documentation, and publishing updates.