On Tue, Sep 9, 2014 at 12:30 AM, Hervé Pagès wrote:
> On 09/08/2014 06:42 PM, Michael Lawrence wrote:
>
>> Instead of printing out multiple lines of a table that is rarely of
>> interest, could we develop Peter's idea toward something like:
>>
>> hg19:chr1 hg19:chr2 ...
>> [lengths ...]
>>
>> No
On 09/08/2014 06:42 PM, Michael Lawrence wrote:
Instead of printing out multiple lines of a table that is rarely of
interest, could we develop Peter's idea toward something like:
hg19:chr1 hg19:chr2 ...
[lengths ...]
Not sure what condensed notation would be useful for circularity.
I don't k
Instead of printing out multiple lines of a table that is rarely of
interest, could we develop Peter's idea toward something like:
hg19:chr1 hg19:chr2 ...
[lengths ...]
Not sure what condensed notation would be useful for circularity.
On Mon, Sep 8, 2014 at 5:21 PM, Peter Hickey wrote:
> Per
Perhaps it might be useful to have some way of highlighting if any of the
chromosomes are circular or highlighting if there are multiple genomes present?
Otherwise this information might be hidden in the "�"
Cheers,
Pete
On 09/09/2014, at 9:44 AM, Herv� Pag�s wrote:
> On 09/08/2014 02:28 PM,
I have a package on the development build called riboSeq; my biological
collaborators have since informed me that this name might cause
confusion as this is also the standard name for particular sequencing
techniques. Is it possible to easily change the name of this package?
Best regards,
Tom
On 09/08/2014 02:28 PM, Peter Hickey wrote:
Just a vote for still allowing for multiple genomes in a Seqinfo object (in a
GRanges object). My use case is in bisulfite-sequencing experiments where there
is often a spike-in of a lambda phage genome along with the genome of interest
(human or mou
Just a vote for still allowing for multiple genomes in a Seqinfo object (in a
GRanges object). My use case is in bisulfite-sequencing experiments where there
is often a spike-in of a lambda phage genome along with the genome of interest
(human or mouse). It's often useful to keep all data from a
On 09/08/2014 11:41 AM, Michael Lawrence wrote:
I might have requested the genome annotation, but I'm pretty sure it
wasn't me who decide on tracking it on a per-sequence basis.
OK, maybe. Don't trust my memory too much on this. No regrets though.
I think it was the right thing to do ;-) Just b
fyi Martin found a bug with the treatment of list data (ie, Number =
'.') in the header. Working on a fix ...
Val
On 09/08/2014 08:43 AM, Gabe Becker wrote:
Val,
That is great. I'll check this out and test it on our end.
~G
On Mon, Sep 8, 2014 at 8:38 AM, Valerie Obenchain mailto:voben...@
I might have requested the genome annotation, but I'm pretty sure it wasn't
me who decide on tracking it on a per-sequence basis. I could imagine use
cases for that though, e.g., when diagnosing sequencing contamination (like
human vs. mouse). But most other tools and file formats expect a single
g
On Mon, Sep 8, 2014 at 1:50 PM, Hervé Pagès wrote:
> Hi Vince,
>
> Yes it would make sense to have the "show" method report the genome
> when genome(x) contains a unique non-NA value. I think the main
>
i would propose that it show selectSome(unique(genome(x))) -- seems
consistent with the multi
Hi Vince,
Yes it would make sense to have the "show" method report the genome
when genome(x) contains a unique non-NA value. I think the main
use case for having the genome defined at the sequence level instead
of the whole object level is metagenomics. Maybe Michael has some other
good use cases
Val,
That is great. I'll check this out and test it on our end.
~G
On Mon, Sep 8, 2014 at 8:38 AM, Valerie Obenchain
wrote:
> The new writeVcf code is in 1.11.28.
>
> Using the illumina file you suggested, geno fields only, writing now takes
> about 17 minutes.
>
> > hdr
> class: VCFHeader
> s
The new writeVcf code is in 1.11.28.
Using the illumina file you suggested, geno fields only, writing now
takes about 17 minutes.
> hdr
class: VCFHeader
samples(1): NA12877
meta(6): fileformat ApplyRecalibration ... reference source
fixed(1): FILTER
info(22): AC AF ... culprit set
geno(8): GT
For GRanges x, my naive expectation is that genome(x) returns a length-
one tag identifying the genome to which chromosomal coordinates
correspond. The genome() method seems to have sequence-specific
semantics, which makes sense, but when we identify sequence
with chromosome, it seems too comp
Michael,
Tags could work. Another approach would be to update the repository and
then look in the log to see if the version number was changed in the most
recent commit. In a sense this is the converse of what our GRANBase package
does when locating historical package versions within the Bioc SVN
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