DReichLab / DReichLab/AdmixTools

arithmetic overflow for latest AADR on systems with 32 bit long

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Dominant language
C
Stars
235
Forks
76
PR merge metrics
No merged PRs in 30d

Description

I am trying to use convertf on the latest version of the AADR (v62.0_1240k_public) and have been running into some issues. Whenever I run convertf -p parconv where parconv is:

genotypename:    v62.0_1240k_public.geno
snpname:         v62.0_1240k_public.snp
indivname:       v62.0_1240k_public.ind
outputformat:    ANCESTRYMAP
genotypeoutname: test.ancestrymapgeno
snpoutname:      test.snp
indivoutname:    test.ind

I run into the following error message:

parameter file: parconv
genotypename: v62.0_1240k_public.geno
snpname: v62.0_1240k_public.snp
indivname: v62.0_1240k_public.ind
outputformat: ANCESTRYMAP
genotypeoutname: test.ancestrymapgeno
snpoutname: test.snp
indivoutname: test.ind
read failure (length mismatch): Success
fatalx:
(inpack) bad data read (length mismatch) 2147479552 1140154008
Aborted

This is rather strange as I am using a file from a source that should be all good (literally from the Reich Lab). Any ideas what may be causing this issue?

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First steps

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  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the convertf -p parconv command with the shown AADR files on a system with a 32-bit long. Trace the inpack bad data read and length-mismatch failure; the issue is done when conversion completes successfully without the arithmetic overflow or read error.

Written by the indexing model from the issue text.

Assessment

Tech stack
c
Domain
cli, tooling
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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