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
- Read the whole issue, then the project's contributing guide.
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- Fork the repository and make your change on a branch.
- 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.
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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