feat(genome): GTF-derived splice-junction insertion into Genome + SA (Phase 17.X)#5

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ewels wants to merge 9 commits into

feat/transcriptome-samfrom

feat/transcriptome-sam-sj-insertion

Commits on Apr 22, 2026

feat(junction): splice motif classifier for sjdb insertion

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feat(junction): compute sjdb shift_left / shift_right for junctions

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feat(junction): PreparedJunction + prepare_junction pipeline

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chore(simplify): reuse detect_splice_motif / encode_motif in sjdb_insert

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feat(junction): sort + cross-strand dedup for prepared junctions

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feat(junction): build_gsj() — concatenated SJ flanking-sequence buffer

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feat(junction): write sjdbInfo.txt + sjdbList.out.tab

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feat(genome): Genome::append_sjdb() — extend forward + rebuild RC

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feat(index): wire sjdb insertion into GenomeIndex::build + extended diff harness

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