DReichLab / DReichLab/EIG

mergeit - output snpname NULL

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C
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Description

I am running eigensoft 6.0.1 and have been trying to run the mergeit command. The two datasets I am combining were converted from plink format successfully using convertf.

Here is what triggered the error:

#=== merge
echo "geno1: hmp.packedancestrymapgeno" > par3.par
echo "snp1: hmp.snp" >> par3.par
echo "ind1: hmp.ind" >> par3.par
echo "geno2: mom02.packedancestrymapgeno" >> par3.par
echo "snp2: mom02.snp" >> par3.par
echo "ind2: mom02.ind" >> par3.par
echo "genotypeoutname: hmgo.packedancestrymapgeno" >> par3.par
echo "snpoutname: hmgo.snp" >> par3.par
echo "indivoutname: hmgo.ind" >> par3.par
mergeit -p par3.par

And the output from mergeit:
parameter file: par3.par
geno1: hmp.packedancestrymapgeno
snp1: hmp.snp
ind1: hmp.ind
geno2: mom02.packedancestrymapgeno
snp2: mom02.snp
ind2: mom02.ind
genotypeoutname: hmgo.packedancestrymapgeno
snpoutname: hmgo.snp
indivoutname: hmgo.ind
packed geno read OK
packed geno read OK
numsnps: 243237 numindivs: 2278
*** warning output snpname NULL
snpname: (null) 243237
indname: (null) 2278
gname: (null)
packedancestrymap output
##end of mergeit run

Looking at the C-code it appears this error is triggered when snpname is not defined. However, it is defined in the output of the mergeit command.

Any thought? Thanks!

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  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 mergeit invocation with par3.par and the listed input files, then inspect the C code path that emits “output snpname NULL.” Compare the parameter names shown in the command output with the values used by that path. Done means mergeit preserves the configured output names instead of reporting NULL.

Written by the indexing model from the issue text.

Assessment

Tech stack
c
Domain
bioinformatics, cli
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
30/100

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