[BioC] GenomicFeatures more detail.

[Fabrice Tourre]

Dear list,

I fellow a paper to annotate a snp in which part of a gene. I firstly
think that GenomicFeatures transcriptsBy method. But it seems
transcriptsBy canno do such more detail check. Does anyone have some
suggestion? Thanks. The define of annotaion is fellow in the paper.

1, First (non-coding) exon. If the gene has at least 2 exons, this is the
part of the first exon that is not located inside the CDS. If the
gene has only one exon, we do not consider it to have a first exon.

2, First intron. If the gene has at least 2 exons, this the intron
following the first exon, provided that it is not located inside
the CDS. Otherwise there is no first intron.

3, Noncoding exon. This is any part of an exon located outside
the CDS region and excluding the first and last exons.

4, External intron. This is an intron located outside the CDS
region and excluding the first and the last introns.

5, Coding exon. This is any part of an exon located inside the
CDS region. Note that exons containing the translation start or
stop generally contain both coding exon and noncoding (or
first/last) exon. Coding SNPs were further subdivided into
synonymous and nonsynonymous, according to their annotation
in dbSNP.

6, Internal intron. This is an intron located inside the CDS region.

7, Last intron. If the gene has at least 2 exons, this is the intron
preceding the last exon, provided that it is not located inside
the CDS. Otherwise there is no last intron.

8, Last (noncoding) exon. If the gene has at least 2 exons, this is
the part of the last exon that is not located inside the CDS.
Otherwise there is no last exon.