Changes in version 2.1.1 (2026-10-18)                  

  - Fixed a compiler warning from GCC 16 (-Wstringop-overflow).

                 Changes in version 2.1.0 (2026-10-16)                  

  - shaman_shuffle_hic_track() is about 6x faster; results are unchanged
    for the same seed.
  - The sort_uniq step of the shuffle (used by
    shaman_shuffle_hic_track()) counts contacts in memory instead of
    with sort | uniq -c: 44 to 3.5 min on chr1 of a Hi-C dataset.
  - Scoring no longer needs perl or temporary files and is about 2x
    faster on dense regions; scores are unchanged.
  - Scoring needs less memory (peak virtual memory 16-36GB instead
    of 48-77GB with shaman 2.0 for dense 5Mb matrices) and can use
    several threads with options(shaman.score.threads = N); scores are
    unchanged.
  - shaman_score_hic_mat_for_track() accepts vectors of matrices;
    matrices in the same row share one read of each track.
  - shaman_shuffle_hic_track(), shaman_shuffle_hic_mat_for_track() and
    shaman_shuffle_and_score_hic_mat() take a seed argument for
    reproducible shuffles. shaman_shuffle_hic_track() stores each
    chromosome's seed, time-based ones included, in the track attribute
    seed; shaman_shuffle_hic_mat_for_track() returns the seed it used
    (NA when it did not shuffle) instead of 0 or 1, and no longer fails
    with "object 'ret' not found" when sort_uniq = FALSE and the matrix
    is not shuffled; shaman_shuffle_and_score_hic_mat() returns the seed
    as seed.
  - SGE mode (options(shaman.sge_support = 1)) works again with current
    misha.
  - shaman_shuffle_hic_track() no longer fails after importing the track
    because the shaman.debug option was missing.
  - The shuffler no longer writes one value past the end of a buffer
    when smoothing the decay curve; results are unchanged.
  - The shuffler no longer kills the R session (division by zero) on
    fewer than 10,000 contacts: a small chromosome or contig in
    shaman_shuffle_hic_track(), or a sparse region in
    shaman_shuffle_and_score_hic_mat().
  - The shuffler stops with an error when it cannot write its output
    (e.g. a full disk) instead of leaving a truncated file.
  - shaman_score_hic_track() stops with an error naming the matrices
    that still have no score after 3 rounds, instead of resubmitting
    them forever; the finished scores stay in work_dir, so a rerun
    computes only the missing ones.
  - A matrix whose expected has fewer contacts than k_exp gets no scores
    (as with fewer than k) instead of failing with "Cannot find more
    nearest neighbours than there are points".
  - library(shaman) no longer tries to unpack the example database.
  - The unused shaman.ks_pl option was removed from shaman.conf;
    configuration files that still set it load as before.
  - shaman now requires R >= 4.0.0 and a C++17 compiler.
  - shaman_get_test_track_db() returns a small example database
    (chr2:176.5e06-177e06 of the previous one), built in the session's
    temporary directory; shaman_get_test_track_db(full = TRUE) returns
    the full one, downloaded from the lab's public S3 bucket into the
    user cache on first use (its md5 is checked), in a form current
    misha can open. The package no longer includes the 104MB database,
    and the examples run on the small one.
  - Gviz is suggested instead of required;
    shaman_plot_tracks_and_annotations() and
    shaman_plot_map_score_with_annotations() need it.
  - The shuffle, score and feature grid functions restore the misha
    options they set (gmultitasking, gmax.data.size), and
    shaman_plot_feature_grid() restores par().
  - The shuffler writes its progress through R's console instead of
    directly to stderr.
  - Multi-core mode (options(shaman.mc_support = 1)) uses
    parallel::mclapply() and no longer registers doMC as the foreach
    backend (doMC is no longer a dependency). Code of your own that ran
    %dopar% on the backend shaman had registered now runs sequentially,
    with foreach's warning; register a backend yourself.
  - The random 1-10s wait before each chromosome's shuffle now happens
    only in SGE jobs, not in multi-core mode or in direct calls of
    shaman_shuffle_hic_mat_for_track().
  - In multi-core and SGE mode, shaman_shuffle_hic_track() stops before
    importing the track when a chromosome's shuffle fails (an error, or
    its process killed, e.g. for memory), and keeps the shuffled
    chromosomes in work_dir so that a rerun shuffles only the rest.
    Before, it imported the track without the failed chromosomes (in
    multi-core mode also without the others scheduled in the same
    process) and deleted the work.
  - The usage article runs on the full example database, and its figures
    are made by the code it shows (precomputed, so the vignette builds
    without it).
  - The map plots use linewidth instead of size for their axis lines, so
    ggplot2 no longer warns that size is deprecated; shaman now requires
    ggplot2 >= 3.4.0.