This PR addresses a bug that broke column ordering in get_gambl_metadata, but also it adds new functionality to calculate the proportion of genome altered (PGA) by CNV and to adjust sample ploidy based on the PGA. The new functions work in both projections (grch37 and hg38), operate on single- or multi-sample files, and have an option to read the file from a local path if necessary.
This PR addresses a bug that broke column ordering in get_gambl_metadata, but also it adds new functionality to calculate the proportion of genome altered (PGA) by CNV and to adjust sample ploidy based on the PGA. The new functions work in both projections (grch37 and hg38), operate on single- or multi-sample files, and have an option to read the file from a local path if necessary.