Source: ga4gh/ga4gh-bed#2, which pulls from michaelmhoffman/ga4gh-bed@7f13c7f

[Rebased onto mainline latexmk infrastructure changes.]

Add BEDv1.pdf to Makefile.
Departures from previous practice in this repository:

- [overrides LATEXMK_ENGINE] I developed the document with `lualatex`
  (included in TeX Live) as I usually do instead of `pdflatex`, because it
  fixes some warts especially in font selection and is where I understand
  TeX engine development has been focused for years. If necessary, I could
  change the font setup to use `pdflatex` instead.

add BED to `MAINTAINERS.md`

add version details from BEDv1.ver rather than using gitinfo2

add fallback `\providecommand` for `\Ac`

hack package `acronym` hyperlink using option `nohyperlinks` instead
make acronym list single-spaced and align to longest acronym

Addresses public comments received on samtools#570:

- [x] change the field separator to not include newline or carriage return ([thanks](#issuecomment-857452438) @simonbrent)
- [x] "line feed" -> "newline" ([thanks](#issuecomment-857452438) @simonbrent)
- [x] "carriage-return" -> "carriage return" ([thanks](#issuecomment-857452438) @simonbrent)
- [x] define "newline" on first use as `'\n'` ([thanks](#issuecomment-857452438) @simonbrent)
- [x] clarify that when `chromEnd` is equal to `chromStart` represents a zero-length feature, which is a feature between two bases such as an insertion. `chromStart=0`, `chromEnd=0` represents an insertion before the first nucleotide of a chromosome ([thanks](#issuecomment-857460372) @simonbrent)
- [x] specify that fields, including custom fields, can only be empty when a single tab is used as the delimiter ([thanks](#issuecomment-857475922) @pdl)
- [x] specify that field data is ASCII printable characters only---the range `'\x20'` to `'\x7e'` ([thanks](#issuecomment-857475922) @pdl)
- [x] `name`: change regex so that it cannot be empty ([thanks](#issuecomment-857475922) @pdl)
- [x] `score`: clarify that `0` should be used in BED5+ files where a `score` attribute of features would be uninformative ([thanks](#issuecomment-857475922) @pdl)
- [x] `strand`:
  - [x] clarify that `.` is the default value, and that a parser should treat BED5 files as if they have `strand=.`
  - [x] explicitly specify that it cannot be empty in a BED6+ file ([thanks](#issuecomment-857475922) @pdl)
- [x] `thickEnd`: clarify that the field is not specified but `thickStart` is means BED files that are not BED8+ ([thanks](#issuecomment-857475922) @pdl)
- [x] change "null or empty" to only "empty" ([thanks](#issuecomment-857475922) @pdl)
- [x] add recommendation to use colorblind-friendly color schemes, and especially to avoid red-green color schemes ([thanks](#issuecomment-857788414) @JspSrs)
- [x] sorting:
  - [x] add that arbitrary orderings of `chrom` are allowed as long as all lines with the same `chrom` value occur consecutively ([thanks](#issuecomment-857955521) @ZhenyuZ)
  - [x] specify that multiple features with the same `chrom`, `chromStart`, and `chromEnd` may appear in any order
- [x] add a section, before "UCSC track files", discussing information that is supplied out-of-band. This should include
  - [x] which of the first 4-12 fields are standard BED fields and which are custom fields ([thanks](#issuecomment-857475922) @pdl)
  - [x] genome assembly used
  - [x] semantics of `score`, `itemRgb`, thick vs. thin positions, block vs. non-block positions
  - [x] definitions of custom fields
  - [x] whether tab is the only delimiter between fields ([thanks](#issuecomment-857475922) @pdl, [thanks](#issuecomment-857508028) @andrewyatz)
- [x] add acknowledgments to any of the folks thanked in the above checklist, with full name and affiliation

Additionally, define "field separator", remove form feed and vertical tab from valid field separators, specify "data line" instead of "line" in several places, and correct some places where boldface was not used but should be.

Co-authored-by: Michael Hoffman <[email protected]>

…0210830 draft]

* Update BEDv1.tex

* polished edits

* Edits in response to public comments 2021-06-28 through 2021-07-09

* Edits in response to public comments 2021-06-28 through 2021-07-09 fix typo

* Edits in reponse to GA4GH PRC

* line edit

* Edits in response to public comments 2021-07-09

* further line edits and footnote fixing

* fix texlint issues

* WIP address uninformative/default/empty issues

* fix empty/uninformative issues

* clarify language on BED fields not being empty

* add special-case `diff/BEDv1.pdf` target that uses lualatex

* fix minor typo

Co-authored-by: Michael Hoffman <[email protected]>

* replace `user` with more specific terms; addresses comment on samtools#570

* move part of `Custom fields` description from recommendation to specification

* add constraint on whitespace in custom fields; addresses comment on samtools#570

* change definition of character and string to use printable characters

* exclude Character and String from comma-separated lists

* define `BED field` and `custom field` as terminology and use them when possible

* clarify definition of BEDn+; addresses comment on samtools#570

…bles

No longer have a hard-coded special command line for this target.

Add `LATEXDIFF_ENGINE` variable to serve the same purpose
as `LATEXMK_ENGINE` but for latexdiff.

in new `Discrete genomic feature data files` heading