Right now, seqwish will treat softmasked bases as not matching non-softmasked bases. These are represented as lower and upper case. Although you can prepare the input for seqwish like this: awk '/^>/ { print } !/^>/ {print toupper($0)}', doing so is annoying and will confuse users. It should be that seqwish defaults to internally upper-casing things, but optionally can be told that it's working on something other than DNA, in which case it shouldn't.
Right now, seqwish will treat softmasked bases as not matching non-softmasked bases. These are represented as lower and upper case. Although you can prepare the input for seqwish like this:
awk '/^>/ { print } !/^>/ {print toupper($0)}', doing so is annoying and will confuse users. It should be that seqwish defaults to internally upper-casing things, but optionally can be told that it's working on something other than DNA, in which case it shouldn't.