parse vs parse2 difference in default behavior for --flip?

[bskubi]

Until recently, I'd been using pairtools parse. Recently I switched to parse2. In testing my parse2-based pipeline, I started running into issues with sorting where, for example, I'd have a (chr1, chr16) pair in one section of the .pairs file and (chr16, chr1) in another section. The problem appears to be resolved now that I started using the --flip parameter.

I don't think this was ever an issue when I used parse, and I don't think I used the --flip parameter with parse. So I'm wondering if possibly pairtools has a different default value for the --flip parameter for parse vs. parse2? The documentation isn't clear on this (and could stand to be a bit more clearly worded, as this is a bit ambiguous:

--flip, --no-flip
If specified, do not flip pairs in genomic order and instead preserve the order in which they were sequenced.

I can infer that '--no-flip' is what this sentence means when it says "if specified", but I would have worded it something like:

--flip, --no-flip
If --no-flip is specified, do not flip pairs in genomic order and instead preserve the order in which they were sequenced. [default: --flip]

I think it would be great if the documentation wording could be cleared up and if the default values for these parameters could be stated.