v1.4.0

What's Changed

• Fix chain_fragmented_hits and add blastn e-value parameter with detailed logging by @Copilot in #31
• WIP: Add BLAST support by @Adamtaranto in #30
• Add HMM update mode and gzip genome support to seed command by @Copilot in #36
• feat: Add tirmite search command for ensemble search with hit merging by @Copilot in #37
• Fix asymmetric blast hit pairing for non-canonical query orientations and add --pairing-map support by @Copilot in #39
• Feature: Extract external flanking sequences with --flank-len by @Copilot in #40
• Fix false "Subject file not found" error when using BLAST database prefix with --blast-db by @Copilot in #42
• Add outer-edge hit anchoring filter to tirmite search by @Copilot in #44
• Standardise CLI argument names to kebab-case across legacy, seed, pair, and search modules by @Copilot in #46
• feat(seed): add --blastdb and pre-computed blast-hits input options; remove --max-gap by @Copilot in #48
• Prevent timeout on long-running BLAST jobs; add progress logging and configurable timeout by @Copilot in #50
• Add MkDocs documentation site for gh-pages by @Copilot in #52
• Refine flank reporting: element count in filenames, paired-only flank output with element IDs by @Copilot in #57
• Bump actions/checkout from 4 to 6 by @dependabot[bot] in #55
• Bump actions/setup-python from 5 to 6 by @dependabot[bot] in #54
• Add target site reconstruction to tirmite pair and new tirmite validate subcommand by @Copilot in #53
• Downgrade negative distance log messages from WARNING to DEBUG by @Copilot in #59
• Log extraction progress for blastdb and indexed genome hits by @Copilot in #63
• Add explicit --insertion-site flag to tirmite pair by @Copilot in #61
• Add cross-model overlap filtering and improve hit filtering documentation for tirmite search by @Copilot in #67
• Fix incorrect flank reporting: only external flanks, per-pair output, split paired TIR files, summary reports, pairing-map model filtering, rename --report to --gff-report, rename --gff-out to --gff, add startup logging, sequence counts in output filen... by @Copilot in #65
• Add split paired output, pairing map model filtering, filter summary report, and fix max-offset filter for asymmetrical model pairs in tirmite search by @Copilot in #69
• Update changelog and citation metadata for v1.4.0 by @Copilot in #71

New Contributors

• @dependabot[bot] made their first contribution in #55

Full Changelog: v1.3.0...v1.4.0