order of mat and pat

[olympus-terminal]

When running merqury, the maternal then paternal haplotypes are supplied as command line arguments. Does merqury use the positions of these args for anything, or would it produce the same results if hap1 and hap2's order were swapped?

[arangrhie]

Hello @olympus-terminal,

The first input haplotype will be drawn in red, second in blue. Results should be identical, except for the coloring in the plots.