option --dovetail or --no-dovetail

[carl-]

I found that in the online manual for bowite 2.2.9, there is an option --dovetail but in the help message of bowtie2 program, there is no --dovetail but a --no-dovetail option.
I also found that the 'gDovetailMatesOK' is false by default in file bt2_search.cpp#L10.

may I set 'gDovetailMatesOK' to true by enable --dovetail ?

and perhaps the online manual or the program help message should be updated .

[BenLangmead]

At some point in the past, we got mixed up about this. Bowtie 2 actually has both --dovetail and --no-dovetail arguments but, as you point out, dovetailing is disabled by default. So specifying --no-dovetail does nothing to change the default. Specifying --dovetail turns it on, so this should be the option documented in the usage message. We are working to fix this. But in the meantime, you ought to be able to use --dovetail

[BenLangmead]

This is fixed in 2.3.1.