Closed roelj closed 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.
%na%
is now package-private in StructuralVariantAnnotation, and also included in libgridss.R
in recent GRIDSS releases.
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 togridss_breakpoint_filter
, which callsis_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.