straw flips output columns x and y based on chromosome names

[TriLab-bioinf]

Hi,

When I use straw function to extract observed contacts between two chromosomes, the returned x and y columns are flipped based on the position of the sorted chromosome names. For instance for the command below, x column should hold the coordinates of chromosome 2R and column y the coordinates of chromosome 2L. However, they are flipped (x = 2L coords and y = 2R coords).

contacts.df <- strawr::straw(norm = norm, fname = hic,
              chr1loc = "2R", chr2loc = "2L",
              unit = dist_unit, binsize = bin_size, matrix = matrix)

If, instead, I set chr1loc = "2L" and chr2loc = "2R", then I get the expected behavior: x = 2L coords and y = 2R coords.

This behavior causes several issues with the analysis downstream. Would it be possible to change this behavior or at least have straw to return the actual chromosome names as column names rather than x and y?

Thanks

Hernan