[EMBOSS] SAM format

[Stephen Taylor]

Hi again Peter,

> On 01/20/11 09:17, Stephen Taylor wrote:
>
>> Is there a bug in the gff3 output of fuzznuc?
>>
>> ##gff-version 3
>> ##sequence-region chr21 1 46944323
>> #!Date 2011-01-20
>> #!Type DNA
>> #!Source-version EMBOSS 6.3.1
>> chr21   fuzznuc nucleotide_motif        13362906        13362942        37.000  +       .       ID="chr21.1";note="*pat pattern"
>>
>> It would be nice to actually show the pattern matched in the note field.
>
> or both. What it shows is the "name" of the pattern, which usually
> defaults to pattern.

Please can you define 'usually' i.e. What are the 'rules' for getting it to show the pattern? Usual behaviour when I run 
it, is it shows note="*pat pattern".

Thanks,

Steve