Repair the chromosome-streaming PIC_counting(load_full = FALSE) path, including empty chromosomes, chromosome-local counting, and restoration of the input peak order.
Make the DAR artifact threshold explicit and configurable. Counts strictly above artifact_threshold are treated as unreliable; the remaining counts are capped at the model-supported value of 5.
Accept both base and sparse matrices consistently in insertion-rate helpers.
Binarize dense and sparse inputs correctly in get_r_by_ct_mat_pq() and add stable convergence and input validation.
Expand automated tests, package metadata, and continuous integration checks.
Declare the R.utils runtime dependency required by data.table::fread() when reading gzip-compressed fragment files.