aligner core: annotated-junction stitching, alignEndsType, in-recursion length penalty - #146

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BenjaminDEMAILLE wants to merge 18 commits into

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BenjaminDEMAILLE:bd/aligner-core-faithfulness

Commits on Aug 26, 2026

feat(junction): sjA-addressable junction table + STAR binarySearch2 find()

BenjaminDEMAILLE
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claude
committed
46725fd
feat(align): carry sjA tags through the window and take STAR's annotated-junction shortcut

BenjaminDEMAILLE
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claude
committed
6aa87c4
feat(align): snap non-canonical annotated junctions onto their annotated coordinates

BenjaminDEMAILLE
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claude
committed
d57245d
feat(params): six more STAR align knobs, alignInsertionFlush Right, read-length mismatch cap

BenjaminDEMAILLE
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claude
committed
ce07526
feat(align): alignSoftClipAtReferenceEnds

BenjaminDEMAILLE
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claude
committed
86232a3
feat(align): apply the genomic-length penalty inside the recursion, not after it

BenjaminDEMAILLE
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claude
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c940baf
feat(test): annotated-junction differential tier, plus alignTranscriptsPerReadNmax

BenjaminDEMAILLE
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claude
committed
4ed0dbb
docs: drop the extend-to-end divergence note, superseded by #145

BenjaminDEMAILLE
and
claude
committed
b4a3219
fix(junction): a one-base intron is a junction, and an annotated gap is never a deletion
BenjaminDEMAILLE
committed
6b85e5a
fix(align): break primary ties on genomic span, as STAR does
BenjaminDEMAILLE
committed
74f5fbe
fix(seed): reproduce STAR's flagDirMap shortcut and chain-loop bound
BenjaminDEMAILLE
committed
bc17033
fix(align): keep sjA in the window-alignment dedup key
BenjaminDEMAILLE
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9cb8980
docs(changelog): record the aligner-core faithfulness results
BenjaminDEMAILLE
committed
3f35d1a
docs(divergence): correct the tie-break entry and the residual list
BenjaminDEMAILLE
committed
99f101d
fix(seed): compare a genome spacer as the larger byte, as STAR does
BenjaminDEMAILLE
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24f7210
docs: fold the spacer-comparison fix into the results
BenjaminDEMAILLE
committed
17fb377
docs(divergence): trace the remaining PE pair to the seed search
BenjaminDEMAILLE
committed
d0c17b4
test(surface): the seven aligner-core knobs are accepted now
BenjaminDEMAILLE
committed
9fc5d04

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aligner core: annotated-junction stitching, alignEndsType, in-recursion length penalty - #146

aligner core: annotated-junction stitching, alignEndsType, in-recursion length penalty#146
BenjaminDEMAILLE wants to merge 18 commits into
scverse:mainfrom
BenjaminDEMAILLE:bd/aligner-core-faithfulness

Commits on Aug 26, 2026

feat(junction): sjA-addressable junction table + STAR binarySearch2 find()

feat(align): carry sjA tags through the window and take STAR's annotated-junction shortcut

feat(align): snap non-canonical annotated junctions onto their annotated coordinates

feat(params): six more STAR align knobs, alignInsertionFlush Right, read-length mismatch cap

feat(align): alignSoftClipAtReferenceEnds

feat(align): apply the genomic-length penalty inside the recursion, not after it

feat(test): annotated-junction differential tier, plus alignTranscriptsPerReadNmax

docs: drop the extend-to-end divergence note, superseded by #145

fix(junction): a one-base intron is a junction, and an annotated gap is never a deletion

fix(align): break primary ties on genomic span, as STAR does

fix(seed): reproduce STAR's flagDirMap shortcut and chain-loop bound

fix(align): keep sjA in the window-alignment dedup key

docs(changelog): record the aligner-core faithfulness results

docs(divergence): correct the tie-break entry and the residual list

fix(seed): compare a genome spacer as the larger byte, as STAR does

docs: fold the spacer-comparison fix into the results

docs(divergence): trace the remaining PE pair to the seed search

test(surface): the seven aligner-core knobs are accepted now