hDOM reference map for HG002 v1.1 (Nb.BssSI, 200 bp/pixel)

Source code for the hDOM pipeline, which assigns single single DNA moleceuls to chromosomal loci from two-channel optical maps. Candidates are generated by an FFT correlation scan and by maligner, then re-ranked by a windowed backbone correlation with a per-window shift, multiplied by a label-set F1 that penalises false-positive and false-negative labels symmetrically and ignores label brightness. Includes per-image adaptive label detection, arc-length straightening, a random-position null giving a per-molecule log P, a runnable example, and a test suite. Requires Python 3.9 or later, an NVIDIA GPU with CuPy, and maligner_dp.