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CGATOxford / UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets
MIT License
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{ts} documentation update #433

Closed TomSmithCGAT closed 4 years ago

TomSmithCGAT commented 4 years ago

When filtering against a whitelist with extract, no longer need to supply --filter-cell-barcode and --whitelist, just the later. Note that former option remains but is hidden from user in --help text and will raise an U.info to inform the user this option is no longer required. See #411 for motivation

Also adding a specific doc page to walk through the network-based deduplication. This is following an email conversation with a user who pointed out some inadequacies/inconsistencies in the way the methods were described across the original CGAT blog post/GR publication/command-line documentation.

TomSmithCGAT commented 4 years ago

Also now checks that string patterns are not longer than read length and if so, outputs more understandable error (see #424 for motivation)

TomSmithCGAT commented 4 years ago

Nothing else in the open issues for documentation/minor debugs etc so this branch is ready for review