Update indelpost to fix realignment bug

[aroon-color]

aldy/aldy/indelpost/pileup.pyx

Lines 653 to 656 in 0849a25

	genome_aln_pos = ref_start + aln.reference_start
	aligned_read_len = (aln.read_end - aln.read_start)
	window_len = window * 6

Hi @inumanag

There's a known bug in this indelpost function that was fixed/worked around about 2 years ago: https://github.com/stjude/indelPost/blob/ecad282eada13e6bb7e54c4b6fe5d32808cca233/indelpost/pileup.pyx#L654-L656

Could you either update the vendored indelpost to the latest release from St Judes or cherrypick this change in? We have a number of samples that reliable trip this particular indelpost bug, where it will correctly run ~10-15% of the time but fail the remainder of times. For example, for this one sample (which I'm happy to provide via email):

for i in $(seq 0 20); uvx --with-requirements $PWD/3rdparty/aldy/requirements.txt aldy genotype --profile illumina -g ugt1a1 --cn=1,1 --output run.$i.aldy --genome hg19 sample.bam

17 of the runs fail with:

🐿  Aldy v4.7 (Python 3.13.1 on macOS 15.3.1)
   (c) 2016-2025 Aldy Authors. All rights reserved.
   Free for non-commercial/academic use only.
Genotyping sample sample.bam...
Trace back error: 0.
ERROR: gene= ugt1a1, file= sample.bam
AttributeError("'NoneType' object has no attribute 'count'")
Traceback (most recent call last):
  File ".cache/uv/archive-v0/cV0mTG-moBE_x3g4pb_YH/lib/python3.13/site-packages/aldy/__main__.py", line 122, in main
    _genotype(args.gene, output, args)
    ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^
  File ".cache/uv/archive-v0/cV0mTG-moBE_x3g4pb_YH/lib/python3.13/site-packages/aldy/__main__.py", line 443, in _genotype
    run(None)
    ~~~^^^^^^
  File ".cache/uv/archive-v0/cV0mTG-moBE_x3g4pb_YH/lib/python3.13/site-packages/aldy/__main__.py", line 393, in run
    _ = genotype(
        gene_db=gene,
    ...<8 lines>...
        **{k: v for k, v in params.items() if v is not None},
    )
  File ".cache/uv/archive-v0/cV0mTG-moBE_x3g4pb_YH/lib/python3.13/site-packages/aldy/genotype.py", line 186, in genotype
    sample = sam.Sample(gene, profile, sam_path, reference, debug)
  File ".cache/uv/archive-v0/cV0mTG-moBE_x3g4pb_YH/lib/python3.13/site-packages/aldy/sam.py", line 117, in __init__
    norm, muts = self._load_sam(path, reference, debug)
                 ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^
  File ".cache/uv/archive-v0/cV0mTG-moBE_x3g4pb_YH/lib/python3.13/site-packages/aldy/sam.py", line 168, in _load_sam
    self._realign_indels(tmp, sam, reference)
    ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^
  File ".cache/uv/archive-v0/cV0mTG-moBE_x3g4pb_YH/lib/python3.13/site-packages/aldy/sam.py", line 499, in _realign_indels
    valn = VariantAlignment(  # type: ignore
        v,
    ...<4 lines>...
        exact_match_for_shiftable=exact_match_for_shiftable,
    )
  File "aldy/indelpost/varaln.pyx", line 169, in aldy.indelpost.varaln.VariantAlignment.__cinit__
  File "aldy/indelpost/varaln.pyx", line 299, in aldy.indelpost.varaln.VariantAlignment._VariantAlignment__parse_pileup
  File "aldy/indelpost/varaln.pyx", line 1165, in aldy.indelpost.varaln.grid_search
  File "aldy/indelpost/pileup.pyx", line 788, in aldy.indelpost.pileup.retarget
  File "aldy/indelpost/pileup.pyx", line 788, in aldy.indelpost.pileup.retarget
  File "aldy/indelpost/pileup.pyx", line 659, in aldy.indelpost.pileup.retarget
AttributeError: 'NoneType' object has no attribute 'count'

and 3 create the expected UGT1A1 result:

🐿  Aldy v4.7 (Python 3.13.1 on macOS 15.3.1)
   (c) 2016-2025 Aldy Authors. All rights reserved.
   Free for non-commercial/academic use only.
Genotyping sample XH2W3GDMX2_CHE-003710-A7_CGCTGTTGAC-CAAGAATTGG.bam...
Potential UGT1A1 gene structures for XH2W3GDMX2_CHE-003710-A7_CGCTGTTGAC-CAAGAATTGG:
   1: 2x*1 (confidence: 100%)
Potential major UGT1A1 star-alleles for XH2W3GDMX2_CHE-003710-A7_CGCTGTTGAC-CAAGAATTGG:
   1: 2x*1 (confidence: 100%)
Best UGT1A1 star-alleles for XH2W3GDMX2_CHE-003710-A7_CGCTGTTGAC-CAAGAATTGG:
   1: *1 / *1 (confidence=100%)
      Minor alleles: *1, *1
UGT1A1 results:
  - *1 / *1
    Minor: [*1] / [*1]
    Legacy notation: [*1] / [*1]
    Estimated activity for *1: unknown
    Estimated activity for *1: unknown