cfDNAlab 0.2.0

cfDNAlab 0.2.0

BREAKING CHANGES:

The output formats are changed to simplify downstream work in R and python. While the previous NumPy .npy format was easy to load in python, the user had to infer the column names, etc. We are moving towards more self-contained formats for a better and safer experience.

• cfdna lengths now outputs a wide-format Zstandard-compressed TSV (.tsv.zst) file with one row per window/group. This is readable by pandas in Python and fread(cmd = "zstd -dc file.tsv.zst") in R.
• cfdna lengths writes command settings to <prefix>.length_settings.json.
• cfdna lengths adds --decimals to control written count precision.
• cfdna midpoints now outputs profiles as a self-contained Zarr store at <prefix>.midpoint_profiles.zarr.
• cfdna midpoints writes command settings to <prefix>.midpoint_settings.json.
• cfdna ends now outputs dense and sparse motif counts as a self-contained Zarr store at <prefix>.end_motifs.zarr.
• cfdna ends writes command settings to <prefix>.end_settings.json.
• cfdna ref-gc-bias now writes the public reference GC package as <prefix>.ref_gc_package.zarr.
• cfdna gc-bias now writes the public sample correction package as <prefix>.gc_bias_correction.zarr.

Any GC-correction packages previously computed are no longer compatible. Please recompute.

Python and R packages for downstream loading:

While the new .zarr format has many benefits, such as being self-contained and working in both R and Python, it's not the easiest to work with in its raw form. We added both an R package and a Python package with friendly loaders and data frame + array getters.

• Adds the Python cfDNAlab package for loading the .zarr outputs of the CLI tool and extracting data frames, meta data, etc. See the cfDNAlab/py-cfdnalab/ directory.
• Adds the R cfDNAlab package for loading the .zarr outputs of the CLI tool and extracting data frames, meta data, etc. See the cfDNAlab/r-cfdnalab/ directory.

Other changes:

• Adds zarrs=0.23.11 dependency.
• Adds downstream Zarr compatibility checks for Python and R reader packages.
• We no longer expose the former gen_cli_docs binary that is for internal use only.