VRS 2.0 Allele RLE representation on VCF annotation

[ahwagner]

VRS 2.0 alleles can normalize to Reference Length Expressions. We should discuss what this looks like for our VCF annotator.

[theferrit32]

I've implemented this in PR #589 and this substitution variant (ref included) is an example used in tests there:

chr19	82664	.	C	T	50	PASS	VRS_Allele_IDs=ga4gh:VA.esmv8nARRRdSysDFuIErJxRAdUSVsWNE,ga4gh:VA.b9AIUegs1SOYO7nKY8l01yllkyUns-u4;VRS_Starts=82663,82663;VRS_Ends=82664,82664;VRS_States=C,T;VRS_Lengths=1,.;VRS_RepeatSubunitLengths=1,.	GT:PS:DP:ADALL:AD:GQ	0/1:.:154:0,0:0,0:120

https://github.com/ga4gh/vrs-python/blob/26eeba3e99f065e2db331b48d62f56e9a6647eef/tests/extras/data/test_vcf_expected_output.vcf#L239C1-L240C1

And for some proper ReferenceLengthExpressions in repeating regions:
https://github.com/ga4gh/vrs-python/blob/26eeba3e99f065e2db331b48d62f56e9a6647eef/tests/extras/data/test_rle.vcf

The expected values are checked here rather than in an annotated vcf file checked into git:

vrs-python/tests/extras/test_annotate_vcf.py

Lines 263 to 311 in 26eeba3

	deletion_variant = variants[0]
	assert deletion_variant.chrom == "1"
	assert deletion_variant.pos == 100210778
	assert deletion_variant.ref == "AA"
	assert deletion_variant.alts == ("A",)
	# Check VRS attributes for deletion
	assert "VRS_Allele_IDs" in deletion_variant.info
	assert "VRS_Starts" in deletion_variant.info
	assert "VRS_Ends" in deletion_variant.info
	assert "VRS_States" in deletion_variant.info
	assert "VRS_Lengths" in deletion_variant.info
	assert "VRS_RepeatSubunitLengths" in deletion_variant.info
	# Expected values for deletion RLE
	# REF: AA uses RLE with length=2, repeatSubunitLength=2
	# ALT: A uses RLE with length=1, repeatSubunitLength=1
	vrs_lengths = deletion_variant.info["VRS_Lengths"]
	vrs_repeat_lengths = deletion_variant.info["VRS_RepeatSubunitLengths"]
	assert len(vrs_lengths) == 2 # REF and ALT
	assert len(vrs_repeat_lengths) == 2
	assert vrs_lengths == (2, 1) # REF: AA (length 2), ALT: A (length 1)
	assert vrs_repeat_lengths == (
	2,
	1,
	) # REF: AA as repeat unit of length 2, ALT: A as repeat unit of length 1
	# Test variant 2: Duplication (CTTT>CTTTCTTT)
	# Expected: length=8, repeatSubunitLength=4
	duplication_variant = variants[1]
	assert duplication_variant.chrom == "1"
	assert duplication_variant.pos == 102995989
	assert duplication_variant.ref == "CTTT"
	assert duplication_variant.alts == ("CTTTCTTT",)
	# Check VRS attributes for duplication
	assert "VRS_Allele_IDs" in duplication_variant.info
	assert "VRS_Lengths" in duplication_variant.info
	assert "VRS_RepeatSubunitLengths" in duplication_variant.info
	# Expected values for duplication RLE
	# REF: CTTT uses RLE with length=4, repeatSubunitLength=4
	# ALT: CTTTCTTT uses RLE with length=8, repeatSubunitLength=4
	vrs_lengths = duplication_variant.info["VRS_Lengths"]
	vrs_repeat_lengths = duplication_variant.info["VRS_RepeatSubunitLengths"]
	assert len(vrs_lengths) == 2 # REF and ALT
	assert len(vrs_repeat_lengths) == 2
	assert vrs_lengths == (4, 8) # REF: CTTT (length 4), ALT: CTTTCTTT (length 8)
	assert vrs_repeat_lengths == (4, 4) # Both are 4-base repeats