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Fix --extra-col-pair example in the docs #272

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Phlya merged 3 commits into from
Oct 22, 2025
Merged

Fix --extra-col-pair example in the docs #272

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991e12e
Fix --extra-col-pair example in the docs
Phlya Jun 27, 2025
cbd3fdf
Update dedup.py
Phlya Jun 27, 2025
a6c1a66
Update pairtools_phase_walkthrough.ipynb
Phlya Aug 20, 2025
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3 changes: 2 additions & 1 deletion pairtools/cli/dedup.py
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Expand Up @@ -160,7 +160,8 @@
"duplicates. Can be either provided as 0-based column indices or as column "
'names (requires the "#columns" header field). The option can be provided '
"multiple times if multiple column pairs must match. "
'Example: --extra-col-pair "phase1" "phase2". [output format option]',
'Example, to dedup phased pairs:'
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@agalitsyna agalitsyna Jun 27, 2025

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Suggested change:

Example for dedup of phased pairs, remove duplicates matching in columns phase1 and (independently) in column phase2. Note how each --extra-col-pair expects a pair of columns as input:

'--extra-col-pair "phase1" "phase1" --extra-col-pair "phase2" "phase2". [output format option]',
)

### Input options:
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