More CLEM fixes#306

Merged

tieneupin merged 14 commits intomainfrom

Jun 19, 2024

Commits on Jun 12, 2024

Improved CLEM context logic to handle repeat positions and their ensuing file names
tieneupin
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Added documentation for some functions in rsync.py
tieneupin
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Commits on Jun 18, 2024

Removed commented out function

tieneupin
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d-j-hatton
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