DReichLab / DReichLab/AdmixTools

Some issue about the software

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C
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Description

I meet some problem when I used qpDstat.
Some of my genotype data:
292229222299999999999999999999999999999999999999101919999999999999
999229229999299999292999292929992199090092222929222929222229922229
999229229991299999222229291209991222222222222229222222222222222229
999229229992229229222299222229992229222221111019222222222222222222
999229229992229229222222222229992229222222222229222220191112222222
SNP data:
scaffold_0:25599 0 0 25599 C T
scaffold_0:26840 0 0 26840 C T
scaffold_0:27901 0 0 27901 C A
scaffold_0:27953 0 0 27953 T A
scaffold_0:27992 0 0 27992 G A
individual data:
GSA1 U GSA
GSA2 U GSA
GSA3 U GSA
GSA4 U GSA
GSA5 U GSA
GSA6 U GSA
GSA7 U GSA
GSA8 U GSA
GSA9 U GSA
Besides, my genotype data have 786 scaffolds. When I run the commond qpDstat -p Dsta_par, it tells some problems:
qpDstat: parameter file: Dsta_par

THE INPUT PARAMETERS

##PARAMETER NAME: VALUE
genotypename: 66inds_SNP.eigenstratgeno
snpname: 66inds_SNP.snp
indivname: 66inds_SNP.ind
popfilename: list_pop1

qpDstat version: 755

warning: bad chrom: scaffold_0:14883 0 0 14883 C T
warning: bad chrom: scaffold_0:15074 0 0 15074 G T
warning: bad chrom: scaffold_0:15222 0 0 15222 C T
warning: bad chrom: scaffold_0:25526 0 0 25526 C T
warning: bad chrom: scaffold_0:25579 0 0 25579 C T
warning: bad chrom: scaffold_0:25599 0 0 25599 C T
warning: bad chrom: scaffold_0:26840 0 0 26840 C T
warning: bad chrom: scaffold_0:27901 0 0 27901 C A
warning: bad chrom: scaffold_0:27953 0 0 27953 T A
warning: bad chrom: scaffold_0:27992 0 0 27992 G A
Segmentation fault (core dumped)

Please tell me what's wrong with my data?
Thank you very much.

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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 qpDstat crash with Dsta_par and the referenced 66inds_SNP.eigenstratgeno, 66inds_SNP.snp, 66inds_SNP.ind, and list_pop1 inputs. Inspect qpDstat's chromosome parsing around the reported scaffold_0 warnings; done means identifying the malformed-input or parsing condition that causes the segmentation fault and confirming the command completes safely.

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
25/100

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