cfDNAlab 0.3.0

BREAKING CHANGES:

• Major refactor of the rust library. Makes a clearer boundary of what is public/private. While cfDNAlab is primarily a CLI tool, the library side needed a clean up. This does not affect CLI usage.

Other changes:

• Adds --motifs-file to cfdna ends for pre-specifying the motifs to count. This allows counting larger motifs without exploding the memory.
• In cfdna lengths, the max_soft_clips cap is only applied when --clip-mode adjust.
• In cfdna ends, fixes theoretical bug that wrongly filtered fragments when kmer-size was larger than read sequence but reference was used as source.

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r-cfDNAlab 0.3.0

• Adds support for schema v2 end-motif Zarr stores written by cfdna ends --motifs-file, including outputs where the motif axis contains user-defined motif groups instead of concrete motif labels.
• Adds the common motifs/motif_idxs, groups/group_idxs, and window_idxs selectors to the sparse_counts_matrix() and dense_counts_matrix functions.
• ends: Improves error message when sparse data has no counts.

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py-cfDNAlab 0.3.0

• Adds support for schema v2 end-motif Zarr stores written by cfdna ends --motifs-file, including outputs where the motif axis contains user-defined motif groups instead of concrete motif labels.
• ends: Improves error message when sparse data has no counts.