Converted *.ancestrymapgeno still a binary file
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Description
I successfully installed CONVERTF and it worked fine (it works when converting example files).
However, when converting datasets in https://reich.hms.harvard.edu/datasets, something is wrong:
The *.ancestrymapgeno file, after the conversion is still a binary file instead of a string file.
For example, I tried to convert Fernandes, Sirak et al. Nature 2020 (https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/Caribbean192v435.zip), the par file is:
genotypename: MDE_paper.geno
snpname: MDE_paper.snp
indivname: MDE_paper.ind
outputformat: ANCESTRYMAP
genotypeoutname: MDE_paper.ancestrymapgeno
snpoutname: MDE_paper.snp
indivoutname: MDE_paper.ind
And the output on command line is:
parameter file: ./par.PACKEDANCESTRYMAP.ANCESTRYMAP
genotypename: FernandesNEE2020_PAM.geno
snpname: FernandesNEE2020_PAM.snp
indivname: FernandesNEE2020_PAM.ind
outputformat: ANCESTRYMAP
genotypeoutname: FernandesNEE2020_PAM.ancestrymapgeno
snpoutname: FernandesNEE2020_PAM.snp
indivoutname: FernandesNEE2020_PAM.ind
packed geno read OK
end of inpack
numvalidind: 62 maxmiss: 62001
packedancestrymap output
##end of convertf run
But the final output file (FernandesNEE2020_PAM.ancestrymapgeno) has the same size as the original file (FernandesNEE2020_PAM.geno), and it is still a binary file instead of a string file.
I'm looking forward for your reply.
Many Thanks.
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Research direction
Start by reproducing the conversion with CONVERTF, the supplied parameter file, and the Caribbean192 dataset, then compare the generated .ancestrymapgeno with the original .geno. Trace the ANCESTRYMAP output path and determine why the result remains binary; done means the converted file is a readable string file with the expected contents.
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Assessment
- Tech stack
- c
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100