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