samtools reaheader not mentioned in the SYNOPSIS

[valeriuo]

There is a bottom link in the SEE ALSO section, but the command is not listed at the top of http://www.htslib.org/doc/samtools.html with all the others.

[jkbonfield]

View is in there twice too. :)

These have already been fixed in samtools/samtools#1154 so I think it just needs the man pages regenerating online. I thought I'd done this (or added a PR for it), but apparently not.

[jkbonfield]

I also think it would be nice if the online man page included links to the sub-command man pages in-situ as they're being listed in the COMMANDS section. They SEE ALSO has links, as does the synposis.

There is custom code to spot these in the synposis section:

elsif ($synopsis && /^(\S+)\s+(\S+)/ && -e "doc/$1-$2.1.html") {

Perhaps we should be looking for .TP followed by .B subcommand too so we can add them there as well.

[jmarshall]

I don't think I got around to pushing it to manconvert yet but a while back I was making a companion script to facilitate spraying these hyperlinks around.

The other even better approach is to add some groff_man markup for it, that could be .deed to nothing at the top of the file but that manconvert could easily recognise. I recently learnt .UR/.UE are conventional for hyperlinks.

[valeriuo]

These have already been fixed in samtools/samtools#1154 so I think it just needs the man pages regenerating online. I thought I'd done this (or added a PR for it), but apparently not.

Yes. It was more of a reminder to check for these issues, once we decide to make next release.