[Bioperl-l] A picky question about "fasta.qual" files

[Nancy Hansen]

Hi!

	I've been doing a lot of qual file reading with SeqIO lately, and
am bothered by the fact that qual.pm assumes a space at the end of each
line (i.e., following the last quality value on each line).  Is this a
standard that I've just never picked up until now?  In any case, I've been
given qual files with no space at the end of each line, and the
PrimaryQual object SeqIO returned has joined qualities, e.g. '5161' where
51 was the last quality on the first line, and 61 the first on the next
line, etc.

	It seems like qual.pm could check for the space at the end of the
line, and add it if it doesn't exist, just to forgive (and make
parsable) the qual files that were created without knowledge of this
standard.

	Thanks,
	--Nancy

*************************************
Nancy F. Hansen, PhD	nhansen at nhgri.nih.gov
Bioinformatics Group
NIH Intramural Sequencing Center (NISC)
8717 Grovemont Circle, Rm. 152L
Gaithersburg, MD 20877
Phone: (301) 435-1560	Fax: (301) 435-6170