cool2matrix has an assumption about the number and the order of chromosomes, but there is no description

[hisakatha]

cool2matrix assumes that the number of chromosomes of your sample is equal to that of the human genome and the order is numerically ascending.

hicrep/R/cool2matrix.R

Lines 26 to 43 in e485dfa

	chr2index <- function(chr) {
	if (substr(chr, 1, 3) == 'chr') {
	chr = substr(chr, 4, nchar(chr))
	}
	if (chr == 'X') {
	index = 23
	}
	else if (chr == 'Y') {
	index = 24
	}
	else if (chr == 'M') {
	index = 25
	}
	else {
	index = as.integer(chr)
	}
	return(index)
	}

However, there is no description about the assumption in the ?cool2matrix document.
Workaround is using a numerical index of your target chromosome at chr argument of cool2matrix to avoid conversion based on the assumption.