[Bioperl-l] Announce: Bio::Seq::Quality

[Heikki Lehvaslaiho]

Marc,

See if the new version of Bio::Seq::Quality works the way you like.

On Thursday 14 July 2005 16:54, Marc Logghe wrote:
> Personally I'd use that optionally by setting/resetting a padding flag
> or something. I'd more be interested in having a way to validate your
> Bio::Seq::Quality one way or another. In de case padding is switched
> off, I'd like to know whether my sequence length is exactly the same as
> my quality array. Does that make sense ?

> In conclusion I'd opt for a inconsistency check and an optional padding
> feature.


I've finished restructuring Bio::Seq::MetaI classes so that they not any
more automatically pad with empty values or truncate meta values to
sequence length. This older behaviour can be activated by setting
force_flush() true.


These new methods have been added to Bio::Meta::MetaI:

force_flush()
meta_length()
named_meta_length()
is_flush()


Since Bio::Seq::Quality has two meta sets with explicit names
('quality', 'trace'), these new methods are in place, too:

quality_is_flush()
quality_length()
trace_is_flush()
trace_length()


Enjoy,

 -Heikki