Bedtools problem with get_rg_cns.R

[jsmedmar]

Best regards,

I'm on version v6.3.2 and I was reviewing the work done by the script get_rg_cns.R.

I realized that the vector cn_estimates, which is the main output, contained always only NA values, indicating that the estimation for small copy number segments was not working.

BRASS/perl/share/Rscripts/get_rg_cns.R

Line 426 in dd0e1c1

seg_cn[i:j] = cn_estimates

After further investigation, I realized that bedtools was not returning headers expected by get_rg_cns.R, specifically seg_coords were not included in the output of the bedtools coverage system call--resulting in coverages being a vector of NA values:

BRASS/perl/share/Rscripts/get_rg_cns.R

Lines 401 to 402 in dd0e1c1

	names(coverage_of_coord) = paste(res[,2], res[,3], sep = "-")
	coverages = coverage_of_coord[seg_coords]

I noticed that on release v6.3.4 you make a reference to stack collision errors, and I wonder if that means this same bug I'm encountering.

Thank you so much in advance.