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PapenfussLab / StructuralVariantAnnotation

R package designed to simplify structural variant analysis
GNU General Public License v3.0
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Missing %na% function in Bioconductor release version #28

Closed roelj closed 4 years ago

roelj commented 4 years ago

I'm using GRIDSS 1.8.1 as part of HMF's pipeline v4.8.

In the gridss_somatic_filter.R script, there's a call to gridss_breakpoint_filter, which calls is_small_inversion_with_homology. That function uses the %na% function.

When using the Bioconductor version of StructuralVariantAnnotation, this function cannot be found. When using the latest version from this Github, the function can be found.

d-cameron commented 4 years ago

%na% was removed from the StructuralVariantAnnotation package as it was a util function not related to structural variants. You'll need install the StructuralVariantAnnotation package from from the prebioconductor branch of github.com/PapenfussLab/StructuralVariantAnnotation using devtools::install_github or update to a more recent HMF pipline release.

d-cameron commented 4 years ago

%na% is now package-private in StructuralVariantAnnotation, and also included in libgridss.R in recent GRIDSS releases.