AttributeError: 'CollapsedCalls' object has no attribute 'consolidate' | version 4.2.1

[leone93]

Version : Truvari v4.2.1

Describe the bug :
2024-02-11 15:51:37,661 [INFO] Truvari v4.2.1
2024-02-11 15:51:37,662 [INFO] Command /home/fabbial/truvari/bin/truvari collapse --gt het --chain -i sample_merged.vcf.gz -o truvari_merge.vcf -c truvari_collapsed.vcf -f /home/fabbial/reference/all.chrs.con.fasta
2024-02-11 15:51:37,669 [INFO] Params:
{
"input": "sample_merged.vcf.gz",
"output": "truvari_merge.vcf",
"collapsed_output": "truvari_collapsed.vcf",
"reference": "/home/fabbial/reference/all.chrs.con.fasta",
"keep": "first",
"bed": null,
"gt": "het",
"intra": false,
"median_info": false,
"debug": false,
"refdist": 500,
"pctseq": 0.95,
"minhaplen": 50,
"pctsize": 0.95,
"pctovl": 0.0,
"typeignore": false,
"hap": false,
"chain": true,
"no_consolidate": true,
"null_consolidate": null,
"sizemin": 50,
"sizemax": 50000,
"passonly": false,
"chunksize": 500,
"bSample": null,
"cSample": null,
"sizefilt": 50,
"no_ref": false
}
2024-02-11 15:51:37,676 [WARNING] Unresolved SVs (e.g. ALT=) are filtered when --pctseq != 0
Traceback (most recent call last):
File "/home/fabbial/truvari/bin/truvari", line 8, in
sys.exit(main())
^^^^^^
File "/home/fabbial/truvari/lib/python3.11/site-packages/truvari/main.py", line 105, in main
TOOLSargs.cmd
File "/home/fabbial/truvari/lib/python3.11/site-packages/truvari/collapse.py", line 799, in collapse_main
for call in itertools.chain.from_iterable(map(m_collap, even_smaller_chunks)):
File "/home/fabbial/truvari/lib/python3.11/site-packages/truvari/collapse.py", line 148, in collapse_chunk
if not matcher.chain or not chain_collapse(m_collap, ret, matcher):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fabbial/truvari/lib/python3.11/site-packages/truvari/collapse.py", line 110, in chain_collapse
m_collap.consolidate(cur_collapse)
^^^^^^^^^^^^^^^^^^^^
AttributeError: 'CollapsedCalls' object has no attribute 'consolidate'

Expected behavior :
Working

Example Data :
If applicable/possible, add example data to help recreate your problem.

Additional context :
I tried both installing with python venv (your instruction) and with pip in a clear conda environment. Same results. Operating on svim2 vcf.

[leone93]

Actually I have the same bug with version 4.2.0 but 4.1.0 is working

[ACEnglish]

Hello,

You have exposed a gap in my functional tests' coverage. I have added a putative fix to develop, but it's going to take time to ensure it works while I make synthetic data that reaches that line of code. I will keep you updated.

If you'd like to move ahead and test it, keep me updated on if it works. Alternatively, since this is caused by the--chain parameter, you could presumably run successfully without it.

Thanks
~/Adam English

[leone93]

Thanks for your fast answer.
I can test the dev version, meanwhile. Where can I find it?

Leonardo

[ACEnglish]

The test coverage is complete. There were a couple of more tweaks I had to make to get it to work for the test data.

You can install from develop directly from the repository:

git clone https://github.com/ACEnglish/truvari.git
cd truvari/
python3 -m pip install .

Edit: I'm unsure when I'll cut a release for this since I just put out a patch last week and I'm currently halfway into implementing a new minor release. So I don't know how long you'll have to use develop.

Below are some notes I need to make related to this ticket so I remember them:
The new test example has three deletions where A matches B and B matches C, but A does not match C when --pctseq 0 --pctsize 0.35. Without --chain A and B would be collapsed and C (because A!=C) would be left alone.

chr21    14088112    14088558    A
chr21    14088212    14088828    B
chr21    14088312    14089203    C

Still need tests to reach conditions around e.g. --chain --gt all

Variant C in the test example will be added to the --collapsed-output with metrics of its similarity to Variant B since that's the one that 'pulled' it into the CollapsedCalls.