deepgenomics / deepgenomics/GenomeKit
`apply_variants` with `reference_alignment=True` raises a ValueError
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Description
This script captures a quick reprex:
```
import genome_kit as gk
from genome_kit._apply_variants import apply_variants
genome = gk.Genome('gencode.v41')
interval = gk.Interval("chr1", "-", 50000, 50005, reference_genome=genome)
variants = [gk.Variant.from_string('chr1:50002:A:C', genome)]
seq, _ = apply_variants(genome.dna, variants, interval, reference_alignment=True)
```
This script provides the following ValueError:
```
Traceback (most recent call last):
File "", line 12, in
seq, _ = apply_variants(genome.dna, variants, interval, reference_alignment=True)
File "/lib/python3.10/site-packages/genome_kit/_apply_variants.py", line 198, in apply_variants
raise ValueError("Reference alignment only work on forward strand.")
ValueError: Reference alignment only work on forward strand.
```
Is there a particular reason that this is only supported on the forward strand? We have a use case that would greatly benefit from being able to generate reference alignments on negative-stranded intervals as well.
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