HelloRanges uses docopt for parsing the argument string
passed as the
cmd argument to functions like
bedtools has its own style of
argument formatting. Here we document the subtle differences.
Here are the specific differences:
docopt requires that multi-character arguments are
prefixed by two hyphens, e.g., --bed. However,
bedtools expects only a single hyphen. It turns out
docopt is robust to the single-hyphen case, except for
the first argument. Since the typical convention is to first
indicate the file, e.g., -a or -i, this
incompatibility does not often arise in practice.
docopt does not allow values of argument to be
bedtools often expects space
separation for multi-valued arguments. As a compromise,
HelloRanges expects the values to be comma-separated. Thus,
-b b.bed c.bed needs to be -b b.bed,c.bed.
Most shells support nested commands within parentheses, e.g.,
-b < (grep foo file.bed), but docopt does not
support that. Instead, nested commands should be enclosed in
double quotes, e.g., -b < "grep foo file.bed". Such
constructs are supported via
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