[Bioc-sig-seq] Minimal short sequences position/orientation container

[Ivan Gregoretti]

Hi everybody,

What is the minimal container class for position-and-orientation of
Solexa reads?


For example, the minimal positional information should be something
like a BED record, like this

chr1\t3000001\t3000036\t\t\t+\t
...(and many more lines)...

sorry for the cumbersome string but I just want to stress that the
minimal information is:

column 1: chromosome
column 2: start
column 3: end
column 6: orientation, either 'plus', 'minus' or undefined. (in this case a '+')

Is there any compact container to load, say, 50 million records? I
thought that RangedData could do that but after reading the
documentation I see that it does not hold strand information.

If there is such container, how do you load it up from a BED file?

Thank you,

Ivan

Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1592
Fax: 1-301-496-9878