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vgteam / giraffe-sv-paper

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readSVvcf is not work in findDups.R #10

Open zhqduan opened 2 years ago

zhqduan commented 2 years ago

Hello,

I want to construct the SV graph from several assemblies. Before starting my own works, I am testing the pipeline according to your manual, first merge SVs from multiple datasets, and then remap-to-dedup-merged-svs. In the second step, when I run the findDups.R, the readSVvcf does not work with the error massage "unused argument (vcf.object = TRUE)". When I remove the parameter "vcf.object=TRUE", the readSVvcf file could work but the command "svs.gr = rowRanges(svs)" gives another error message: 

Error in MatrixGenerics:::.load_next_suggested_package_to_search(x) : 
  Failed to find a rowRanges() method for GRanges objects.

Any suggestions with this issue? Thanks in advance.

Best, Zhongqu

adamnovak commented 2 years ago

I think this is an R package version problem. I think @jmonlong got rid of the vcf.object argument when he bumped the sveval R package version from 1.2.2 to 2.0. So maybe you need to install sveval 1.2.2 for the scripts in this repo to work?

zhoudreames commented 2 years ago

I think this is an R package version problem. I think @jmonlong got rid of the vcf.object argument when he bumped the sveval R package version from 1.2.2 to 2.0. So maybe you need to install sveval 1.2.2 for the scripts in this repo to work?

Yes, I also encountered such a problem, and following your suggestion, I resolved it.

netwon123 commented 1 year ago

sorry, i want to know how to install old version? using docker?

adamnovak commented 1 year ago

It looks like, to install an older version of an R package, you need to either give the full URL for that version's tarball to install.packages, along with repos=NULL, or you need to install the remotes package and use its install_version method. Both of these approaches should be explained at https://stackoverflow.com/q/17082341