Feature/pass reads#361
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* Made a proper SVG thought i'd just include it here * Remove setting the read_number on the result Add in the correct strand classifications for minknow 6 * Remove Read number from Result and all references to read number * Update target versions for MinKNOW to 6.0.0 - 6.0.0 Explicitly exit if running on MInKNOW 5.X.X * Update vendored read until API to v3.5.2 * Update test for conencted base caller version to work * Pin ont-pybasecall-client-lib at 7.4.12 * Add downgrade to 2024.2.0 to error message * Fix bug in reads not unblocking as expected #372 * change list() to [] * Chunk tracker uses read_id not read_number, update trackers internal variable names * bump version to 2024.3.0 * Fix tests for the new MinKNOW version compatibility Fix tests for the _statistics too not use `read_number` * Bump summarise version to 0.2.7 * Drop incorrect gotcha * Feature/deprecate guppy (#374) * This commit addresses the removal of guppy.py, partial removal of guppy tests, edits to documentation to largely replace guppy with dorado, removes the ont-pyguppy-client-lib and adds a warning to the readme. It also adds some extra classes to the read_until init in targets. * Remove builtin module for guppy * Update FAQ questions to focus dorado as well as Guppy * Change validate caller warning to mention dorado not guppy * Change readme warnings to Focus dorado and minknow breaking changes more Add link/requirement for dorado_basecall_server not guppy_basecall_server * Rename tests to dorado validation tests * Add dorado to mappy-test install target
alexomics
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Aug 26, 2024
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alexomics
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Aug 26, 2024
agrima2010
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Apr 17, 2026
* Attempt at using pass_reads * Add message about generating the aligner description * FIX bug where parameter reads was being overwritten by empty list reads * DRAFT Feature/minknow6 compatibility (LooseLab#369) * Made a proper SVG thought i'd just include it here * Remove setting the read_number on the result Add in the correct strand classifications for minknow 6 * Remove Read number from Result and all references to read number * Update target versions for MinKNOW to 6.0.0 - 6.0.0 Explicitly exit if running on MInKNOW 5.X.X * Update vendored read until API to v3.5.2 * Update test for conencted base caller version to work * Pin ont-pybasecall-client-lib at 7.4.12 * Add downgrade to 2024.2.0 to error message * Fix bug where unblocked_read_ids wasn't being written out * Chunk tracker uses read_id not read_number, update trackers internal variable names * bump version to 2024.3.0 * Fix tests for the new MinKNOW version compatibility Fix tests for the _statistics too not use `read_number` * Bump summarise version to 0.2.7 * Drop incorrect gotcha * Feature/deprecate guppy (LooseLab#374) * This commit addresses the removal of guppy.py, partial removal of guppy tests, edits to documentation to largely replace guppy with dorado, removes the ont-pyguppy-client-lib and adds a warning to the readme. It also adds some extra classes to the read_until init in targets. * Remove builtin module for guppy * Update FAQ questions to focus dorado as well as Guppy * Change validate caller warning to mention dorado not guppy * Change readme warnings to Focus dorado and minknow breaking changes more Add link/requirement for dorado_basecall_server not guppy_basecall_server * Rename tests to dorado validation tests * Add dorado to mappy-test install target * Fix black formatting of accepted chunks list * rename read_id to read_number on _generate_action because I may as well * return action from override as for some pythons it doesn't mutate in place * add mappy-rs because I keep typing it and not mappy_rs * Don't clip RF from front, used cached read_id for the result
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pass_readsfunction on the caller, rather than individual calls topass_read, should be faster and has removed sleeping.sub_tagand makes them comments.N.B Committed as @satriobio from the remote Vs code server, is this identity theft?