.snp error in Admixtools
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- Dominant language
- C
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Description
Hi all,
I have a snp file looking like this:
loc7_pos19 APLT01000001.1 0.0 3008 T G
loc7_pos32 APLT01000001.1 0.0 3021 T C
loc7_pos150 APLT01000001.1 0.0 3139 C A
loc7_pos176 APLT01000001.1 0.0 3165 C T
loc7_pos179 APLT01000001.1 0.0 3168 A G
loc7_pos184 APLT01000001.1 0.0 3173 A G
loc16_pos41 APLT01000003.1 0.0 2263 G A
loc16_pos55 APLT01000003.1 0.0 2277 C T
loc18_pos14 KL579098.1 0.0 19491 T C
loc19_pos7 KL579098.1 0.0 38380 G A
loc19_pos22 KL579098.1 0.0 38395 C A
loc21_pos46 KL579099.1 0.0 7699 G T
loc21_pos70 KL579099.1 0.0 7723 G A
But when running qpDstat -p parqpDstat [-l lo] [-h hi] >logfile
I receive this error:
`fatalx:
bad chrom: APLT01000001.1
Aborted`
I don’t understand the problem to solve it, is it because it should be an integer (due to the example.snp) or something else?
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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.
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Research direction
Start by checking qpDstat's SNP-format expectations and comparing the supplied records with example.snp. Reproduce the command using parqpDstat and the shown chromosome value, then determine whether the parser requires numeric chromosome identifiers or supports accession-style names. Done means documenting the accepted format or identifying the required parser change.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- c
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100