Changelog

Changelog for alevin-fry

Unreleased

Currently no unreleased features

0.4.3 - 2021-11-11

Fixed

Fixed a bug that prevented the 1-edit rescue (in generate-permit-list) for barcodes of odd length, when using the unfiltered permit-list filtering mode. Thanks to @Gaura for helping to find and diagnose the issue.

0.4.2 - 2021-10-16

Added

Support for USA mode to the infer command by passing the --usa flag.

Changed

Large internal code re-organization, moving most alevin-fry related functionality out of the libradicl crate / library.
Some details of how cr-like-em works in USA mode. Instead of each splicing status for each gene being completely independent, the expecation of assignment for spliced and unspliced also depend on ambiguous abundance, and ambiguous abundance depends on both spliced and unspliced.

Fixed

Issue #25 where cells with only (and too few) highly-multimapping reads could sometimes prevent quantification from completing successfully when using the cr-like-em mode. Now, such cells are instead flagged and their identifiers are output in quant.json. Generally, these cells will have no expressed genes in the corresponding count matrix.

0.4.1 - 2021-07-22

This is a minor release, intended mostly to bump some version dependencies and to address Issue #22.

Changed

Changed the name of the JSON file written by the quant command from meta_info.json to quant.json to match other commands
Updated versions of crates in dependencies for libradicl and alevin-fry

Removed

The quant command no longer writes a cmd_info.json file