Update on these tasks.
1) XStringSetList now has an nchar() method (as of Biostrings 2.31.17)
2) restrictToSNV() was removed from VariantAnnotation
3) The following generics and methods for VCF and VRanges have been
added to VariantAnnotation 1.9.50:
isSNV()
isInsertion()
isDeletion()
Hi Martin,
On 03/21/2014 01:45 PM, Martin Morgan wrote:
On 03/20/2014 05:20 PM, Hervé Pagès wrote:
Hi,
On 03/19/2014 01:10 PM, Michael Lawrence wrote:
You can apparently use 1D extraction for VCF, which is a little
surprising;
I learned it from restrictToSNV.
This is inherited from
Some of the inconsistency emerges from wrappers that correspond to
operations on the rowData. I think that's fine as long as it's obvious (as
in the case of findOverlaps and isSNV). The head and tail functions are by
convention row-based for rectangular objects. I agree though that if we
keep 1D
On 03/20/2014 05:20 PM, Hervé Pagès wrote:
[...]
Following that logic names(se1) also probably return colnames(se1).
/\
should
H.
H.
On Wed, Mar 19, 2014 at 1:07 PM, Vincent Carey
st...@channing.harvard.eduwrote:
Also, the code for DNAStringSetList is too low-level. There should just be
an nchar,XStringSetList that does the same thing as
nchar,CompressedCharacterList. Then restrictToSNV or whatever just does
any(nchar(x) == 1L) for any List.
Michael
On Wed, Mar 19, 2014 at 1:00 PM, Michael Lawrence
On Wed, Mar 19, 2014 at 4:00 PM, Michael Lawrence lawrence.mich...@gene.com
wrote:
It would be nice to have functions like isSNV, isIndel, isDeletion, etc
that at least provide precise definitions of the terminology. I've added
these, but they're designed only for VRanges. Should work for
You can apparently use 1D extraction for VCF, which is a little surprising;
I learned it from restrictToSNV.
On Wed, Mar 19, 2014 at 1:07 PM, Vincent Carey
st...@channing.harvard.eduwrote:
On Wed, Mar 19, 2014 at 4:00 PM, Michael Lawrence
lawrence.mich...@gene.com wrote:
It would be
Thanks Sean. Probably also need an isSubstitution for any substitution,
either SNV or complex.
On Wed, Mar 19, 2014 at 3:20 PM, Sean Davis sdav...@mail.nih.gov wrote:
On Wed, Mar 19, 2014 at 4:26 PM, Valerie Obenchain voben...@fhcrc.orgwrote:
Thanks for the feedback.
I'll look into nchar
