mergeit - output snpname NULL
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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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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.
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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