Format of alleles in VCF

[d-cameron]

The format of alleles in VCF is not formally defined in the specifications. In particular, the following edge cases exist in the current specifications:
A*A* is a valid alt allele but should not.
A<contig>A is unclear as to whether it is (or should be) valid.

I propose the following grammar productions as a formal definition for the format of alleles:

ref:
 base-string

alt:
 allele
 allele , alt

allele:
 base-string
 missing-allele
 symbolic-allele

missing-allele:
 *

symbolic-allele:
 id-string
 symbolic-insertion
 breakend
 breakpoint

symbolic-insertion:
 base id-string
 id-string base
 id-string

breakend:
 base-string null-allele
 null-allele base-string

breakpoint:
 base-string [ breakpoint-reference [
 [ breakpoint-reference [ base-string
 base-string ] breakpoint-reference ]
 ] breakpoint-reference ] base-string

breakpoint-reference:
 contig-reference
 contig-reference : digits

contig-reference:
 id-string
 contig-identifier

digits:
 digit
 digits digit

digit: one of
 0 1 2 3 4 5 6 7 8 9 0

base: one of
 A C G T N a c g t n

base-string:
 base
 base-string base

id-string:
 < contig-identifier >

contig-identifier:
 string-containing-no-whitespace-or-colon

contig-identifier is a problematic definition. Currently the spec allows [ ] < > . * as part of contig identifiers. Inclusion of the brackets as valid characters are especially likely to cause difficulties with implementations as alleles such as N[<[>[>[ are currently valid, and the string is an ambiguous reference either to a (contig-identifier) reference contig "" or a (id-string) named contig CHR.

[d-cameron]

What is the most appropriate mechanism for contributing to specifications? Provide pull requests? Is there a mailing list for spec discussion?