genome: --genomeTransformOutput SAM reports original coordinates - #160

Open

BenjaminDEMAILLE wants to merge 7 commits into

scverse:mainfrom

BenjaminDEMAILLE:bd/genome-transform-output

Commits on Aug 26, 2026

feat(params): genomeType, genomeTransformOutput, genomeSuffixLengthMax, sjdbInsertSave

BenjaminDEMAILLE
and
claude
committed
0a4cd83
feat(genome): back-transform alignments onto the original genome
BenjaminDEMAILLE
committed
7303d62
feat(genome): wire --genomeTransformOutput SAM through the align paths
BenjaminDEMAILLE
committed
9a10f62
refactor(params): keep only --genomeTransformOutput in this PR
BenjaminDEMAILLE
committed
f9b879b
docs(changelog): --genomeTransformOutput SAM
BenjaminDEMAILLE
committed
5a4332a
test(surface): --genomeTransformOutput is accepted now
BenjaminDEMAILLE
committed
c54c691
style: rustfmt after the rebase
BenjaminDEMAILLE
committed
b6449f3