index out of range error

[NElight]

when i run seqlink, i get index out of range error. it occur when only one variant in some range.

[gaow]

@NElight we are working on a new release with @changebio which should be out within 30 days. Do you have a small toy test data you can share (or email to me privately ) so we make sure our new release works without issue on your test data?

[NElight]

@gaow it is my test vcf file and fam file.
command is "seqlink --fam 3312362.fam --vcf last.vcf.gz --freq gnomAD_genome_AF --build hg19 -o LinkageAnalysis -K 0.0001 --moi AD -W 0 -M 1 -j 0 --run-linkage --debug"
test.zip

[NElight]

@gaow Any new information about the test data?thank u.

[gaow]

@NElight we are still working on the release and @changebio will be able to test it on the toy data as we pack up the release, in a couple of weeks from now. Thanks for your patience.

[changebio]

Hi @NElight @gaow Thank you for your patience. I just released our new version SEQLinkage v2. I have tested your data by the following command line seqlink --fam test/3312362.fam --vcf test/last.vcf.gz --freq gnomAD_genome_AF --blueprint data/genemap.hg19.txt -o LinkageAnalysis -K 0.0001 --moi AD -W 0 -M 1 --chp --run-linkage. You can follow the documentation (https://changebio.github.io/SEQLinkage/) to install and use SEQLinkage v2. Please let me know if you have any questions.

[gaow]

Thanks @changebio great I just saw this. Looks like it works. @NElight we have not yet built a docker image for that release, but @changebio has bumped it to Python 3 and streamlined the dependencies, so it should be easy to install using standard pip/conda commands. Still please let us know if there is an issue.

[NElight]

@gaow @changebio thank u very much

[NElight]

@changebio thank u , i rerun my test data using the new version SEQLinkage v2，get some ValueError.

[changebio]

@NElight The bug has been fixed. Please try following commands.

pip install -u SEQLinkage
rm -rf LinkageAnalysis
#CHP markers
seqlink --fam test/3312362.fam --vcf test/last.vcf.gz --freq gnomAD_genome_AF --blueprint data/genemap.hg19.txt -o LinkageAnalysis_chp -K 0.0001 --moi AD -W 0 -M 1 --run-linkage
#Single variants
seqlink --fam test/3312362.fam --vcf test/last.vcf.gz --freq gnomAD_genome_AF --blueprint data/genemap.hg19.txt -o LinkageAnalysis_var -K 0.0001 --moi AD -W 0 -M 1 --run-linkage --single-marker

Please let me know if you have any further questions.

[NElight]

@changebio thank u , i rerun my test data using the new version SEQLinkage v2，get another error.

[changebio]

Could you send me more details. I cannot repeat your error. Did you get the error form CHP markers and/or single markers? Please show the command you used in the screenshot. @NElight

[NElight]

@changebio i am sorry for my incomplete information. i run the commands that you recommended, that two commands get the same error.

[changebio]

@NElight Sorry about the error you got. I still can not replicate the error after you show me your command. But I know where may go wrong. I add a test line in there. you can update our package again, and run on your computer.

By the way. I attached all the data and results I got by running SEQLinkage v2 on your test data. Please let me know whether it works on your computer or not.
The screen shot is the command I used. I copied genemap.hg19.txt from ~/.SEQLinkage/genemap.hg19.txt.

test.tar.gz