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Nik-Zainal-Group / signature.tools.lib

R package containing useful functions for mutational signature analysis
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errors in genomeChartSV #51

Closed tischfis closed 1 year ago

tischfis commented 1 year ago

two errors;

1)if bedpe file has chromosomes that don't start with "chr", code attempts to match character to non-character object 2) if sv_obj$junctions_catalogue is NULL, will throw an error

andreadega commented 1 year ago

Hi, sorry you had issues with the genomeChartSV function. This plot function is still a draft that will require an update in the future. In any case, I will try to provide a fix in the next days. What value did you use for the "genome.v" parameter? hg19 or hg38?

tischfis commented 1 year ago

hg19. I was easily able to correct the bugs to get the plot function to work but wanted to bring to your attention for a stable release. Happy to provide my fixes if you'd like. Thanks.

andreadega commented 1 year ago

Thanks again for bringing this to our attention. We prefer to add our own fixes, so we make sure we don't introduce conflicts with current dev code, which is in a hidden repository. I will correct the code and hopefully add some other improvements with it if there is time.

andreadega commented 1 year ago

Hopefully this has been fixed now, if not let me know.