Re: [AMOS-help] Some errors in documentation ...

[Dan B. <dan...@gm...>]

I'm trying to dig up my old usage notes on Bambus and I came across this email.

I finally fixed the first of these two minor documentation bugs here:
* https://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus_Manual
* https://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus_Manual&diff=276&oldid=207

I don't know where I originally read about ace2contig, so I can't fix
that (can't find it on the above wiki).


Cheers,
Dan.

On 20 February 2009 14:32, Dan Bolser <dan...@gm...> wrote:
> The line that reads:
>
> "-c <contig_file> . Use a GDE formatted .contig assembly file as
> source of linking information. The .contig files can be obtained
> either from TIGR Assembler output (by concatenating the contents of
> the .align directory) or by converting .ace files (created by phrap or
> Consed) using *the ta2ace package* distributed with AMOS."
>
>
> Should read:
>
> "-c <contig_file> . Use a GDE formatted .contig assembly file as
> source of linking information. The .contig files can be obtained
> either from TIGR Assembler output (by concatenating the contents of
> the .align directory) or by converting .ace files (created by phrap or
> Consed) using *the ace2contig package* distributed with AMOS."
>
>
> Also, the usage information for ace2contig reads:
>
> "-o output prefix (output is <prefix>.contig)"
>
>
> The actual behaviour is "-o output_file_name". I know this last one is
> pedantic, but I don't see why the documentation shouldn't be correct.
>
>
> One other minor point, I had to manually copy $BASEDIR/lib/TIGR into
> my local Perl library path to get bambus working. The installer didn't
> work out that it needed to set 'use lib qw( $BASEDIR/lib )'.
>
>
> Cheers,
> Dan.
>