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v0.7.0
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0.7.0 (2022-08-02)

NOTE

An issue with a bump of the clap crate which changed argument parsing behavior caused some previously optional program arguments (specifically the -t and -m options) to be treated as mandatory. This changed the required argument set for alevin-fry v0.6.0 (and possibly earlier) when it is built from source and when the dependency resolver pulls in the newer version of clap. Unfortunately, a rebuild of crates on bioconda also triggered this behavior, meaning that commands that would previously run with v0.6.0 now require additional arguments to be passed along as they are considered mandatory. A more detailed description of the issue can be found in this Q&A discussion. While the command can be changed to pass these arguments along in previous versions, the proper optional status has been restored in v0.7.0 and it is recommended to upgrade.

⚠ BREAKING CHANGES

  • To simplify and unify the naming convention for UMI resolution methods, the strategy name "full" (as a synonym for "parsimony-em") has been removed. The resolution strategy previous selected by "parsimony-em" or "full" can now only be selected by passing "parsimony-em" as the resolution option.

Other changes

  • Improvements to argument parsing and error propagation.
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