[Bioc-sig-seq] Package ShortRead: occurenceFilter and chromosomeFilter("NM")

[Ivan Gregoretti]

Hello everyone,

When loading reads with ShortRead::readAligned(), one has the great
convenience of filtering the input.

If I intend to load only unique sequences that are unaligned ("NM"),
can I use occurenceFilter?

By _unique_ I mean that if the sequence ATCTCATAGTGGG has been loaded
once, I do not want to load it the next time it is found.


?srFilter clearly documents how aligned reads are occurenceFilter-ed,
however, unaligned reads are not mentioned.

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: 1-301-496-1016 and 1-301-496-1592
Fax: 1-301-496-9878