DReichLab / DReichLab/EIG

Converted *.ancestrymapgeno still a binary file

Open
#61 5 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
C
Stars
207
Forks
61
PR merge metrics
No merged PRs in 30d

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.

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  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 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.

Written by the indexing model from the issue text.

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

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.