Changes in version 1.0.4 (2026-05-19)                  

CRAN submission preparation

  - DESCRIPTION: removed redundant "in R" from the title.
  - DESCRIPTION: expanded acronyms (ATAC-seq, NGS, ChIP-seq) and added a
    reference to the methods paper in the form
    <doi:10.1093/bioinformatics/btae649>.
  - quaqc(): replaced the cat() call that printed the program help with
    a message() call so that it can be suppressed by the user.
  - footprint() and pileup() examples: switched from \dontrun{} to a
    guarded \donttest{} that no-ops when the quaqc binary or a sample
    BAM is unavailable.

                        Changes in version 1.0.3                        

CRAN submission preparation

  - Reverted the footprint() and pileup() examples to \dontrun{} because
    they additionally require a user-supplied BAM file that the user
    must obtain themselves; the previous \donttest{} wrapper caused R
    CMD check --run-donttest to fail. The quaqc() example continues to
    use \donttest{ if (nzchar(Sys.which("quaqc"))) }.
  - Added cran-comments.md to .Rbuildignore.

                        Changes in version 1.0.2                        

CRAN submission preparation

  - Added SystemRequirements: quaqc to DESCRIPTION.
  - Moved options(quaqc.bin = ...) initialisation into .onLoad() in
    R/zzz.R.
  - Migrated inst/CITATION from deprecated citEntry()/personList() to
    bibentry()/c(person(), person()).
  - Updated .Rbuildignore to exclude development files (CLAUDE.md,
    .claude/).
  - Removed empty merge_reports() stub (R/merge.R).
  - Converted \dontrun{} to \donttest{ if (nzchar(Sys.which("quaqc"))) }
    in examples for quaqc(), footprint(), and pileup().
  - Fixed typo genereal → general in DESCRIPTION.

                        Changes in version 1.0.1                        

Bug fixes

  - parse_quaqc(): input validation now checks that all required JSON
    keys are present and reports which are missing, rather than
    accepting any subset of valid names.
  - parse_quaqc(): non-list input now produces a clear error message
    ('json.text' must be a list).
  - parse_quaqc_file(): the length/type guard used && instead of ||,
    allowing numeric length-1 inputs or character length->1 inputs to
    bypass validation and crash inside gzfile().
  - parse_quaqc(): fixed typo fagment_histogram_max →
    fragment_histogram_max in the params key vector; the misspelled key
    was silently absent from $params$integer on every parsed report.
  - parse_quaqc(): removed tss_histogram_max from the params key vector;
    this key is not emitted by quaqc (only tss_histogram_size is), so it
    was silently missing from every parsed report.
  - quaqc(): calling quaqc() with no arguments (to print help) would
    error with object 'version' not found; fixed by returning just the
    help text.
  - quaqc(): when json is a file path, the parsed report was discarded
    and NULL returned; the file connection was also leaked on error.
    Both issues are fixed.
  - quaqc(): when peaks, tss, target.list, or blacklist was supplied as
    a GRanges object, the temporary BED file's on.exit(unlink(...))
    handler lacked add = TRUE; passing more than one GRanges argument
    would leak all but the last temp file.
  - quaqc(): GRanges objects are 1-based inclusive; the BED files
    written from them now correctly use 0-based half-open coordinates
    (start - 1L).
  - quaqc(): verbose = NULL caused an error (argument is of length
    zero); the verbosity block now guards against NULL.
  - melt_reports(): calling with a quaqc object containing failed
    reports caused a crash on NULL subscript-assignment inside the get_*
    helper functions; failed reports are now filtered out automatically
    (with a message).
  - melt_reports(): histogram and TSS-pileup helpers used 1:nRow[i] to
    build row indices, which produces c(1, 0) when a sample has zero
    rows; replaced with seq_len(nRow[i]) throughout.
  - melt_reports(): TSS background normalisation could call rep(0, n)
    with a negative n; clamped to max(0L, n).
  - melt_reports(): dividing TSS depth by nranges when nranges is 0 or
    NA produced Inf/NaN; guarded with a fallback to 1.
  - melt_reports(): use.basename = TRUE failed on R < 4.0 because
    data.frame() converts character columns to factors by default in
    those versions; the Sample column is now explicitly coerced to
    character before basename() is called.
  - pileup(): passing tss in ... previously issued a warning then
    crashed with a confusing "formal argument matched by multiple actual
    arguments" error from R; it now stops with a clear message.
  - footprint(): the unreachable tss-in-... warning (R errors before the
    body runs due to ambiguous partial matching against
    tss.size/tss.qlen/ tss.tn5) has been removed.

Other

  - Added a testthat test suite covering parsing, all 13 melt_reports()
    sections, validators, print snapshots, and input-validation paths.