High-Performance Open-Source Archive
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.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"))) }.cran-comments.md to
.Rbuildignore.SystemRequirements: quaqc to DESCRIPTION.options(quaqc.bin = ...) initialisation into
.onLoad() in R/zzz.R.inst/CITATION from deprecated
citEntry()/personList() to
bibentry()/c(person(), person())..Rbuildignore to exclude development files
(CLAUDE.md, .claude/).merge_reports() stub
(R/merge.R).\dontrun{} to
\donttest{ if (nzchar(Sys.which("quaqc"))) } in examples
for quaqc(), footprint(), and
pileup().genereal → general in
DESCRIPTION.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.testthat test suite covering parsing, all 13
melt_reports() sections, validators, print snapshots, and
input-validation paths.
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