Ac updates#7
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Acribbs merged 56 commits intocribbslab:mainfrom Apr 23, 2025
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Updated setup and entry points. Updated the helper comments on pipeline scripts. Change length filters for reads to max 50kb.
update documentation
default primer use for index splitter updated.
use SMART primer sequence as default and edit script to use first 10bp for pattern matching
Rename file to better reflect function
Rename file to better reflect function
imports for api added correctly
to reflect script name changes
to reflect script name changes
update unittest to current version of primer splitter
The split-fastqcats command was not being called correctly and was failing on integration test. Have editted to to specify the params correctly
update to use correct main function for test
remove redundant argument from parallel_split_reads
Contributor
Author
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@as2110 The tests wont pass, likely due to a problem in the code, would you look at the tests failing and try and work out why they are. Happy to take more of a look when I get time. |
fix last search window based on pattern length instead of window length.
pytests for PrimerSplitter and IndexSplitter classes
Contributor
|
Hi Adam, Have merged these updates and also pushed through some other updates to add some notes to the documentation. Tests passing locally, hopefully passing here too. |
change file extensions to match correct input/outout
add additional unit_test
add note about setting -e threshold
…into AC-updates
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