[dhaupt88]

VariantIdentifier::parse() and DnaSequence throw on alleles that VCF 4.2 explicitly permits: N in REF and ALT, and . as ALT when a site has no alternate allele.
Variant callers emit both, so consumers parsing real VCF data fail on valid lines.
This PR accepts them.

• DnaSequence accepts N, the IUPAC code for any base. complement() already leaves it unchanged.
• The new AlternateAllele extends DnaSequence additionally accepts exactly . and offers isMissing().
• parseDash() and parseCanonical() accept N and an ALT of ., and build an AlternateAllele for ALT.
• The type of VariantIdentifier::$alternate stays DnaSequence, so existing readers keep working.

`.` lives in AlternateAllele, not in DnaSequence, to keep primer and barcode validation strict

DnaSequence also validates primer and index barcode sequences.
. is not sequence content but the VCF missing value, so allowing it there would let . pass as a primer or barcode, with length() 1 and reverseComplement() ..
Only the ALT position of a variant may hold it, see section 1.4.1 of https://samtools.github.io/hts-specs/VCFv4.2.pdf.

For agents 🤖: draft, waiting for review

• make test and make stan pass.
• make rector already fails on master with Undefined constant PHPUnitSetList::PHPUNIT_40; not touched here.
• length() of . stays 1 on purpose, matching what consumers computed with strlen before.

🤖 Generated with Claude Code

[github-code-quality]

Code coverage overview

Languages: PHP

PHP / code-coverage/phpunit

master 2949ba3	allow-n-and-missing-... e013a22	+/-
89%	90%	+1%

View coverage of the 7 most impacted files.

File	master 2949ba3	allow-n-and-missing-... e013a22	+/-
IlluminaSampleS...ingsSection.php	100%	100%	0%
InterOp/RunResult.php	100%	100%	0%
CSVArray.php	90%	96%	+6%
PHPStan/Rules/M...ypehintRule.php	0%	88%	+88%
PHPStan/Rules/M...ypehintRule.php	0%	100%	+100%
PHPStan/Rules/C...ypehintRule.php	0%	100%	+100%
AlternateAllele.php	0%	100%	+100%

ℹ️ Calculations represent line coverage. Results may change as calculations are updated.