numsnps output:0
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- Dominant language
- C
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Description
kai@kai-VirtualBox:~/EIG/CONVERTF$ mergeit -p Final.par
parameter file: Final.par
geno1: NEO.geno
snp1: NEO.snp
ind1: NEO.ind
geno2: Cay.geno
snp2: Cay.snp
ind2: Cay.ind
outputformat: EIGENSTRAT
genooutfilename: merged_output.geno
snpoutfilename: merged_output.snp
indoutfilename: merged_output.ind
numsnps input: 1233013 1151145
eigenstrat output
numsnps output: 0 numindivs: 16
Histogram of checkmatch return codes
total: 0
##end of mergeit: 80.930 seconds cpu 1313.628 Mbytes in use
Hi, I'm encountering this issue in bold when attempting to merge two Eigenstrat files using the mergeit function, the .ind files are showing in the output but both .snp and .geno output files are blank. Please help me fix this, thanks
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the mergeit entry point and the Final.par parameter file, then inspect how NEO.geno/NEO.snp and Cay.geno/Cay.snp are read and how numsnps output is produced. Reproduce the command and compare the input metadata with the generated merged_output.geno and merged_output.snp; done means valid non-empty merged files are produced or the incompatibility is reported clearly.
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Assessment
- Tech stack
- c
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100