It doesn't look like it was the patch - the error is still there. I'll look
in to this some more.
Valerie
On Fri, Mar 15, 2019 at 11:10 AM Valerie Obenchain
wrote:
> Hi Erik,
> I think the problem was introduced in a contributed patch applied to
> VariantAnnotation in devel. I've
Hi Erik,
I think the problem was introduced in a contributed patch applied to
VariantAnnotation in devel. I've reverted the patch and expect
VariantAnnotation (and downstream packages) to clear up on Windows with
tomorrow's builds.
Valerie
On Thu, Mar 7, 2019 at 4:10 AM Erik Fasterius
wrote:
>
Hi developers,
Today is the deadline for updating NEWS files and marks the release
candidate for Bioconductor 3.7. After today, pushes to master should be
bug fixes only.
https://www.bioconductor.org/developers/release-schedule/
Thanks.
Valerie
[[alternative HTML version
The BioC 3.5 branch is now ready.
Remember, you always have access to 2 versions of your package in svn:
the "release" and "devel" versions.
Right now the "release" version of your package (which is not officially
released yet but will be tomorrow if everything goes well) is in the 3.5 branch
package chimeraviz (so far it's in a
separate branch and not commited to Bioconductor). Does the API freeze
mean that I have to wait until the Bioconductor release before I
commit it to the devel branch?
On Fri, Apr 7, 2017 at 2:38 AM, Valerie Obenchain <voben...@gmail.com
<mailto
Hi,
Some recent activity has caused some (red) ripples across the builds and
the El Capitan Mac builds are still unsettled. To accommodate, we're
extending the deadline to pass R CMD build and check with no errors to
next Friday (http://www.bioconductor.org/developers/release-schedule/).
Thanks for the report and reproducible example. Now fixed in 1.14.8 and
1.15.22.
Valerie
On 08/07/2015 07:25 AM, Julian Gehring wrote:
Hi,
When I use the 'filterVcf' function to process a VCF file in chunks, the
output file contains as many copies of the header as there are
chunks.
There is a collection in S4Vectors that test atomic types and return a
logical.
isSingleInteger
isSingleNumber
isSingleNumberOrNA
isSingleString
isSingleStringOrNA
isTRUEorFALSE
isSingleNumber(1:5)
[1] FALSE
isSingleNumber(NA)
[1] FALSE
Val
On 07/22/2015 04:22 PM, Jim Hester wrote:
Not
Hi Julian,
Yes, the behavior is intentional though I hadn't thought of the annoying
chatter in the case of chunking. Sorry about that.
The current readVcf() reads/parses fields according to header
multiplicity and type; fields without headers are skipped. It is on the
TODO to be more
Correction below.
On 07/15/2015 04:14 PM, Valerie Obenchain wrote:
Hi,
BiocParallel in release and devel are quite similar so I'd like to
narrow the focus to before the changes to SnowParam and after. This
means BiocParallel 1.0.3 (R 3.1) vs BiocParallel 1.3.34 (R 3.2.1) which
is the current
) don't seem to support these thoughts.
Or do you interpret these numbers differently?
Best,
Leo
On Sun, Jul 12, 2015 at 11:00 AM, Valerie Obenchain
voben...@fredhutch.org wrote:
Hi Leo,
Thanks for the sample code I'll take a look.
You're right, SnowParam has changed quite at bit - logging
of SnowParam.
Thanks, I'll fix that.
Valerie
On Fri, May 22, 2015 at 5:33 PM, Valerie Obenchain
voben...@fredhutch.org wrote:
Hi,
Thanks for reporting the bug. Now fixed in 1.13.4 (devel) and 1.2.2
(release).
bplapply(1:2, print, BPPARAM=SnowParam(outfile = NULL))
starting worker for localhost:11031
Vince,
On 07/10/2015 04:12 AM, Vincent Carey wrote:
I have had (potentially transient and environment-related) problems with
bplapply
in gQTLstats.
Was the problem during build or check where a man page example or unit
test could be isolated as the problem?
I substituted the foreach
July newsletter available at
http://www.bioconductor.org/help/newsletters/2015_July/
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Email: voben...@fredhutch.org
Phone: (206) 667-3158
___
futile.options_1.0.0bitops_1.0-6
RCurl_1.95-4.6
[13] biomaRt_2.24.0 RSQLite_1.0.0 XML_3.98-1.2
On 06/11/2015 01:55 AM, Valerie Obenchain wrote:
Thanks for the report.
Now fixed in release (1.14.2) and devel (1.3.25).
Valerie
On 06/09/2015 09:44 AM, Robert Castelo wrote:
hi
locateVariants(), predictCoding() and the family of mapToTranscripts()
functions all return strand according to the annotation matched. The
only time the strand of the output could possibly be different from the
strand of the input 'query' is when 'ignore.strand = TRUE' (FALSE by
default).
I
I'll add a section to the BiocParallel docs.
Valerie
On 06/04/2015 07:55 AM, Kasper Daniel Hansen wrote:
Yes, based on the documentation that particular random stream generator
would work with mclapply.
This is absolutely a subject which ought to be covered in the BiocParallel
documentation.
Hi,
Thanks for reporting the bug. Now fixed in 1.13.4 (devel) and 1.2.2
(release).
bplapply(1:2, print, BPPARAM=SnowParam(outfile = NULL))
starting worker for localhost:11031
starting worker for localhost:11031
Type: EXEC
[1] 1
Type: EXEC
[1] 2
Type: DONE
Type: DONE
[[1]]
[1] 1
[[2]]
[1] 2
Poster registration is now open. Visit the web site
http://www.bioconductor.org/help/course-materials/2015/BioC2015/
and registration page
https://register.bioconductor.org/BioC2015/poster_submit.php
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Posters can be from any area of computational biology, medicine,
Now available at http://bioconductor.org/help/newsletters/2015_April/
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On 03/25/2015 07:48 PM, Simon Urbanek wrote:
On Mar 25, 2015, at 3:46 PM, Valerie Obenchain voben...@fredhutch.org wrote:
Hi Simon,
I'm having trouble with nested parallel workers, specifically, forking inside
socket connections.
You simply can't by definition - when you fork *all
On 03/30/2015 02:51 PM, Simon Urbanek wrote:
On Mar 30, 2015, at 4:40 PM, Valerie Obenchain voben...@fredhutch.org wrote:
On 03/25/2015 07:48 PM, Simon Urbanek wrote:
On Mar 25, 2015, at 3:46 PM, Valerie Obenchain voben...@fredhutch.org wrote:
Hi Simon,
I'm having trouble with nested
Hi Simon,
I'm having trouble with nested parallel workers, specifically, forking
inside socket connections.
When mclapply is called inside a SOCK, PSOCK or FORK worker I get an
error in unserialize().
cl - makeCluster(1, SOCK)
fun = function(i) {
library(parallel)
mclapply(1:2, sqrt)
}
On 03/16/2015 05:31 PM, Hervé Pagès wrote:
On 03/16/2015 04:06 PM, Michael Lawrence wrote:
On Mon, Mar 16, 2015 at 3:12 PM, Robert Castelo robert.cast...@upf.edu
mailto:robert.cast...@upf.edu wrote:
+1 IMO BioC could adopt the zero-width ranges representation for
insertions, adapting
Hi Robert,
Thanks for reporting the typo and bug. Now fixed in 1.13.41.
Valerie
On 03/17/2015 10:58 AM, Robert Castelo wrote:
in my message below, the line that it says:
head(loc_all$CDSID)
it should say
head(coding2$CDSID)
cheers,
robert.
==
hi,
On 03/16/2015 05:31 PM, Hervé Pagès wrote:
On 03/16/2015 04:06 PM, Michael Lawrence wrote:
On Mon, Mar 16, 2015 at 3:12 PM, Robert Castelo robert.cast...@upf.edu
mailto:robert.cast...@upf.edu wrote:
+1 IMO BioC could adopt the zero-width ranges representation for
insertions, adapting
Hi Nico,
Can you try again with BiocParallel 1.1.16? Likely related to this post,
https://stat.ethz.ch/pipermail/bioc-devel/2015-March/007114.html
Valerie
On 03/16/2015 07:05 AM, Nicolas Delhomme wrote:
Hej!
Martin I guess that's for you :-) And I suppose it might only be temporary (due
AM, Valerie Obenchain wrote:
Hi Aaron,
Thanks for catching this.
I favor enforcing names in 'assays'. Combining by position alone is too
dangerous. I'm thinking of the VCF class where the genome information is
stored in 'assays' and the fields are rarely in the same order.
Looks like we also need
Hi Aaron,
Thanks for catching this.
I favor enforcing names in 'assays'. Combining by position alone is too
dangerous. I'm thinking of the VCF class where the genome information is
stored in 'assays' and the fields are rarely in the same order.
Looks like we also need a more informative
Hi Thomas, Michael,
makeVRangesFromGRanges has been added to 1.13.34. The
methods-VRanges-class.R file was already large so I added
makeVRangesFromGRanges.R.
A few notes:
- '...' was replaced with 'keep.extra.columns'
- row names are propagated automatically so I removed the explicit
Hi,
Thanks for the report. Now fixed in 1.13.31.
This problem, like the last one you reported, was related to CDSID
becoming an IntegerList. When region=AllVariants, results are combined
and ordered by QUERYID, TXID, CDSID and GENEID. In your example ties
were not broken by QUERYID or TXID
,
robert.
On 02/10/2015 07:37 PM, Valerie Obenchain wrote:
Hi Robert,
This sounds like a good addition. I'll put it on the TODO. If you need
this immediately I'd be happy to accept a patch (with unit tests).
Valerie
On 02/10/2015 06:29 AM, Robert Castelo wrote:
hi,
in the VariantAnnotation
Hi Robert,
This sounds like a good addition. I'll put it on the TODO. If you need
this immediately I'd be happy to accept a patch (with unit tests).
Valerie
On 02/10/2015 06:29 AM, Robert Castelo wrote:
hi,
in the VariantAnnotation package, the help of the functions for
identifying
Hi Robert,
Thanks for reporting this. Now fixed in 1.13.27.
I introduced this bug when switching the coordinate mapping over from
mapCoords() to the new mapToTranscripts() family. The output from the
new mapper is cleaner and allowed me to tidy some old code. In the
process I realized there
Hi all,
Happy 2015. The January 2015 Newsletter is now available:
http://www.bioconductor.org/help/newsletters/2015_January/
Highlights include the (experimental) work being done with Docker
containers, coordinate mapping, the algorithmic changes behind the
overlaps operations and a review
/TSPC-utils.R
SplicingGraphs/vignettes/SplicingGraphs.Rnw
SplicingGraphs/man/assignReads.Rd
SplicingGraphs/man/txpath-methods.Rd
systemPipeR/R/utilities.R
These packages should be clear (of this error) on tomorrow's builds.
Thanks.
Val
On 12/14/2014 09:15 AM, Valerie Obenchain wrote:
Hi Sean
is rectangular and VRanges is ragged, and
there is no established way to encode the raggedness in the VCF.
On Mon, Dec 8, 2014 at 11:27 AM, Valerie Obenchain
voben...@fredhutch.org mailto:voben...@fredhutch.org wrote:
This could be fixed in the VRanges - VCF coercion or in VCF - VRanges.
Currently
, and the user ends up confused. So I agree
with Julian that we should just drop VRangesScanVcfParam and have
readVcfAsVRanges just be an alternative syntax to as(readVcf(), VRanges).
Michael
On Mon, Dec 8, 2014 at 10:48 AM, Valerie Obenchain
voben...@fredhutch.org mailto:voben...@fredhutch.org wrote
Thanks to Michael and Julian for taking care of this. Fixes are in
devel, = 1.13.15.
Valerie
On 12/03/14 08:44, Michael Lawrence wrote:
Looks like an issue when expand()ing the VCF. Maybe Val could take a look?
On Wed, Dec 3, 2014 at 7:39 AM, Julian Gehring julian.gehr...@embl.de
wrote:
(length of GRangesList)
of lists (length of files) of vectors (length of GRanges).
best,
Mike
On Mon, Sep 29, 2014 at 7:09 PM, Valerie Obenchain voben...@fhcrc.org wrote:
Hi Kasper,
The reduceBy* functions were intended to combine data across ranges or
files. If we have 10 ranges and 3 files you
Looks like the test code didn't make it through. Attaching again ...
On 10/27/2014 11:35 AM, Valerie Obenchain wrote:
Hi Kasper and Mike,
I've added 2 new functions to GenomicFiles and deprecated the old
classes. The vignette now has a graphic which (hopefully) clarifies the
MAP / REDUCE
- locateVariants(vcf, txdb, AllVariants())
=
so my question is, should not seqlevelsStyle() also change the 'genome'
slot of the Seqinfo object in the updated object?
if not, would the solution be updating the 'genome' slot in the way i
did it?
thanks!
robert.
On 10/23/2014 11:14 PM, Valerie
Hi Robert,
Thanks for the bug report and reproducible example. Now fixed in release
1.12.2 and devel 1.13.4.
I've also updated the docs to better explain how the Seqinfo objects are
propagated / merged when supplied as 'genome'.
Valerie
On 10/23/2014 06:45 AM, Robert Castelo wrote:
hi
The fourth quarter Newsletter is now available at
http://www.bioconductor.org/help/newsletters/2014_October/
Topics include support for GRCh38, htslib and an introduction to the
biocMultiAssay working group.
Valerie
___
Bioc-devel@r-project.org
] TxDb.Hsapiens.BioMart.igis_2.3 XML_3.98-1.1
[39] xtable_1.7-4 zlibbioc_1.11.1
On Wed, Sep 17, 2014 at 2:08 PM, Valerie Obenchain voben...@fhcrc.org
mailto:voben...@fhcrc.org wrote:
Hi Gabe,
Have you had a chance to test writeVcf? The changes made over the
past week have
Hi,
Import and manipulation of BigWig files in rtracklayer make use of the
Kent C library and are not supported on windows.
This is documented at
?import.bw
?`BigWigFile-class`
This problem isn't specific to an 'over the network' example. Trying to
import() a local BigWig on Windows will
Hi Michel,
In BiocParallel 0.99.24 .convertToSimpleError() now checks for NULL and
converts to NA_character_.
I'm testing with BatchJobs 1.4, BiocParallel 0.99.24 and SLURM. I'm
still not getting an informative error message:
xx - bplapply(1:2, FUN)
SubmitJobs
Hi Kasper,
The reduceBy* functions were intended to combine data across ranges or
files. If we have 10 ranges and 3 files you can think of it as a 10 x 3
grid where we'll have 30 queries and therefore 30 pieces of information
that can be combined across different dimensions.
The request to
example
off-line.
Valerie
On 09/22/2014 02:58 PM, Valerie Obenchain wrote:
Hi Thomas,
Just wanted to let you know I saw this and am looking into it.
Valerie
On 09/20/2014 02:54 PM, Thomas Girke wrote:
Hi Martin, Micheal and Vincent,
If I run the following code, with the release version
Hi Thomas,
Just wanted to let you know I saw this and am looking into it.
Valerie
On 09/20/2014 02:54 PM, Thomas Girke wrote:
Hi Martin, Micheal and Vincent,
If I run the following code, with the release version of BiocParallel then it
works (took me some time to actually realize that), but
).
I'm working on the 'chunking' approach next. It looks like we can still
gain from adding that.
Valerie
On 09/08/2014 12:00 PM, Valerie Obenchain wrote:
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
Hi Herve,
This unit test passes in VA 1.11.30 (the current version in svn). It was
related to writeVcf(), not the IRanges/S4Vector stuff. My fault, not yours.
Val
On 09/09/2014 02:47 PM, Hervé Pagès wrote:
Hi Val,
On 09/09/2014 02:12 PM, Valerie Obenchain wrote:
Writing 'list' data has
/04/14 15:28, Valerie Obenchain wrote:
Thanks Gabe. I should have something for you on Monday.
Val
On 09/04/2014 01:56 PM, Gabe Becker wrote:
Val and Martin,
Apologies for the delay.
We realized that the Illumina platinum genome vcf files make a good test
case, assuming you strip out all
to
reduce it or reduce its
overhead (i.e., the CHARSXP allocation).
Gabe is doing more tests.
On Tue, Aug 26, 2014 at 9:43 AM, Valerie
Obenchain
voben...@fhcrc.org
:33 PM, Valerie Obenchain voben...@fhcrc.org
mailto:voben...@fhcrc.org wrote:
Hi Michael,
I'm interested in working on this. I'll discuss with Martin next
week when we're both back in the office.
Val
On 08/05/14 07:46, Michael Lawrence wrote:
Hi guys (Val, Martin
()
is the absence of the trace function. Instead of having this hard coded
we want to add a BPTRACE arg that allows tracing/debugging for any
BiocParallel function. This should be added over the next week.
Valerie
On 08/06/2014 12:18 PM, Valerie Obenchain wrote:
Hi Jeff,
Thanks
2014 05:12:41 PM PDT, Ryan C. Thompson wrote:
Hi Valerie,
I got really busy around May and never got a chance to thank you for
adding this option to summarizeOverlaps! So thank you!
-Ryan
On Thu 01 May 2014 04:25:33 PM PDT, Valerie Obenchain wrote:
GenomicAlignments 1.1.8 has a 'preprocess.reads
for ... should be updated
to reflect this?
On Wed Aug 6 11:21:20 2014, Valerie Obenchain wrote:
Hi Ryan,
On 08/05/2014 05:47 PM, Ryan C. Thompson wrote:
Hi again,
I'm looking at the examples in the summarizeOverlaps help page here:
http://www.bioconductor.org/packages/devel/bioc/manuals/GenomicAlignments
?).
Thanks,
Jeff
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Fred Hutchinson Cancer Research Center
1100
Hi Michael, Ryan,
Yes, it would be ideal to have a single signature for both cases of
'iterate'. We went over the pros/cons again and at the end of the day
decided to keep things as they are. No perfect solution here.
These were the primary points:
- Disadvantages of defining REDUCER with
/30/2014 02:41 PM, Ryan C. Thompson wrote:
No, I forgot to attach the file. Here is the link:
https://www.dropbox.com/s/7qghtksl3mbvlsl/counting-modes.R
On Wed 30 Apr 2014 02:18:28 PM PDT, Valerie Obenchain wrote:
Hi Ryan,
These sound like great contributions. I didn't get an attachment - did
On 05/01/2014 02:05 PM, Ryan wrote:
Hi Valerie,
On Thu May 1 13:27:16 2014, Valerie Obenchain wrote:
I have some concerns about the *ExtraArgs() functions. Passing
flexible args to findOverlaps in the existing mode functions
fundamentally changes the documented behavior. The modes were
Hi Ryan,
These sound like great contributions. I didn't get an attachment - did
you send one?
Thanks.
Valerie
On 04/30/2014 01:06 PM, Ryan C. Thompson wrote:
Hi all,
I recently asked about ways to do non-standard read counting in
summarizeOverlaps, and Martin Morgan directed me toward
Hi Kevin,
Thanks for the report. The old behavior of as.data.frame on 'RangedData'
objects has been re-instated in IRanges 1.99.7.
Last week we added a new as.data.frame,List method that is now used by
all 'List' objects. This was done for a variety of reasons that I'll
include in an
.
On Wed, Mar 19, 2014 at 3:20 PM, Sean Davis sdav...@mail.nih.gov
mailto:sdav...@mail.nih.gov wrote:
On Wed, Mar 19, 2014 at 4:26 PM, Valerie Obenchain
voben...@fhcrc.org mailto:voben...@fhcrc.org wrote:
Thanks for the feedback.
I'll look into nchar for XStringSetList
We are pleased to announce the first issue of the Bioconductor
newsletter. The aim is to produce this on a quarterly schedule with
updates on core development projects and BioC-related events.
Input on current publications, research updates and items of interest
are welcome (send to
: bioc-devel-boun...@r-project.org
[mailto:bioc-devel-boun...@r-project.org] On Behalf Of Valerie Obenchain
Sent: Tuesday, April 01, 2014 9:36 AM
To: bioconduc...@r-project.org; bioc-devel@r-project.org
Subject: [Bioc-devel] Bioconductor newsletter: April 2014
We are pleased to announce
] sendmailR_1.1-2 stats4_3.2.0stringr_0.6.2
[25] tools_3.2.0 whisker_0.3-2 XML_3.98-1.1
[28] zlibbioc_1.9.0
On Wed, Mar 19, 2014 at 2:00 PM, Valerie Obenchain voben...@fhcrc.org
mailto:voben...@fhcrc.org wrote:
On 03/19/14 10:24, Michael Love wrote:
hi
the yield is ignored.
I've added this info to the 'summarizeOverlaps' and 'readGAlignments'
man pages in GenomicAlignments.
Valerie
On 03/27/14 08:30, Valerie Obenchain wrote:
Hi Mike,
This is fixed in Rsamtools 1.15.35.
The bug was related to when the mate-pairing was performed wrt meeting
://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Valerie Obenchain
Program in Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B155
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: voben...@fhcrc.org
Phone: (206) 667-3158
Fax:(206) 667-1319
again for the input.
Valerie
On 03/11/2014 10:23 PM, Michael Lawrence wrote:
On Tue, Mar 11, 2014 at 3:33 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
On 03/11/2014 02:52 PM, Hervé Pagès wrote:
On 03/11/2014 09:57 AM, Valerie Obenchain wrote:
Hi
Bioconductor runs cleanly.
Can someone please help in figuring out what is going on?
Antti
--
Valerie Obenchain
Program in Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B155
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: voben...@fhcrc.org
Phone: (206) 667
Hi all,
I'm soliciting feedback on the idea of a general file 'registry' that
would identify file types by their extensions. This is similar in spirit
to FileForformat() in rtracklayer but a more general abstraction that
could be used across packages. The goal is to allow a user to supply
and bioc-devel (all packages up to
date 2013-12-07).
Best wishes
Julian
--
Valerie Obenchain
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B155
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: voben
In addition to the resources Martin mentions,
library(GenomicAlignments)
browseVignettes(GenomicAlignments)
gets the 'Counting reads with summarizeOverlaps' vignette. (In the
release branch this vignette lives in GenomicRanges.) The vignette
covers the counting modes in detail and
-Original Message-
From: Valerie Obenchain [mailto:voben...@fhcrc.org]
Sent: 27 November 2013 21:17
To: Becq, Jennifer; bioc-devel@r-project.org
Subject: Re: VariantAnnotation writeVcf problem
Hi,
I can't reproduce this error. Here is a read/write example using a file from
VariantAnnotation
The replacement method for fixed- on a VCFHeader has been added to the
devel version 1.19.17.
Valerie
On 11/20/2013 10:08 AM, Valerie Obenchain wrote:
Correction below.
On 11/20/2013 09:59 AM, Valerie Obenchain wrote:
Hi Delphine,
I've cc'd your message to the Bioconductor mailing list
...@illumina.com
-Original Message-
From: Valerie Obenchain [mailto:voben...@fhcrc.org]
Sent: 20 November 2013 17:28
To: Becq, Jennifer; bioc-devel@r-project.org
Subject: Re: VariantAnnotation writeVcf problem
Hi Jennifer,
I've cc'd your message to the Bioconductor mailing list. We have two lists
Hi Stephanie,
The error is thrown from SeqArray:::.info at line 216 in the file and is
related to the handing of NA values.
x[x == ] - NA
Output from the == comparison can contain NAs and therefore can't be
used (consistently) in subsetting operations.
'x' is a NumericList.
Browse[2] x
Sorry. This was likely my error when I created the replacement methods.
I see you've fixed it in svn, Martin, thanks.
Val
On 11/20/2013 07:00 PM, Michael Lawrence wrote:
Right, match.fun() needs to be within the initial endoapply, not later.
Isn't the convention though to use `obeyQname-` in
Hi Jennifer,
I've cc'd your message to the Bioconductor mailing list. We have two
lists, one for general questions and the other for bug reports/feature
requests. Please post future questions to one of these lists instead of
sending them to a single person. The lists reach a wider audience
will also implement this replacement method ?
Thank you very much for your reactivity.
Best regards.
Delphine.
Le 05/11/13 01:44, Valerie Obenchain a écrit :
Hi Delphine,
In 1.9.5 (devel branch) I've added 'meta-', 'info-' and 'geno-'
replacement methods for VCFHeader.
fl - system.file(extdata
Hi Katsuhito,
I've cc'd your message to the Bioconductor mailing list. We have two
lists, one for general questions and the other for bug reports/feature
requests. Please post future questions to one of these lists instead of
sending them to a single person. The lists reach a wider audience
Michael,
This is implemented in 1.7.48. AD is expanded as a list matrix where
each list element holds a REF,ALT pair.
Val
On 09/05/2013 07:36 AM, Valerie Obenchain wrote:
Hi,
On 09/04/2013 04:23 PM, Michael Lawrence wrote:
Hi, Val,
I just fixed expand,VCF to support multiple 'A' columns
Hi Michael,
This looks like an artifact from reorganizing the subsetting code in
IRanges/XVector. The operation works for me with the most recent
versions from devel. I'm assuming it now works for you?
Valerie
On 09/13/2013 02:33 AM, Michael Love wrote:
hi,
I came across an error in
The 'GroupedIRanges' error is related to some cleanup Herve is doing on
the subsetting code in IRanges/XVector. The error should be gone with
the most recent devel versions (IRanges 1.19.33, XVector 0.1.2,
GenomicRanges 1.13.42). These may take a day to propagate through
biocLite().
Valerie
:
On Fri, Aug 23, 2013 at 8:41 AM, Valerie Obenchain voben...@fhcrc.org
mailto:voben...@fhcrc.org wrote:
Hi Michael,
Martin and I have been discussing this. In addition to the fix you
suggest, what do you think of changing the default to
compressed=TRUE for the RleList constructor
Hi Michael,
Martin and I have been discussing this. In addition to the fix you
suggest, what do you think of changing the default to compressed=TRUE
for the RleList constructor? Rle is the only one of the AtomicLists with
default FALSE. Was there a reason for this when it was first
DEXSeq to those changes.
Best regards,
Alejandro Reyes
Mike, Alejandro,
I also wonder about getting rid of the 'exonID' metadata column. This is
redundant with 'exonic_part_number'. Do you have a preference for keeping one
or the other?
Valerie
On 07/31/2013 10:04 AM, Valerie Obenchain wrote
Hi Nico,
(Adding Mike and Alejandro.)
Because disjointExons() came from DEXSeq I wanted to preserve the
behavior for backwards compatibility and familiarity to DEXSeq users.
There are a couple of changes I'd like to make so disjointExons() is
consistent with the other extractors in
Mike, Alejandro,
I also wonder about getting rid of the 'exonID' metadata column. This is
redundant with 'exonic_part_number'. Do you have a preference for
keeping one or the other?
Valerie
On 07/31/2013 10:04 AM, Valerie Obenchain wrote:
Hi Nico,
(Adding Mike and Alejandro.)
Because
in a seriously faster language, like C++ via Rcpp.
John
On 7/1/13 10:04 PM, Valerie Obenchain wrote:
Hi,
S4 method dispatch can be very slow. Would it be reasonable to cache the
most
recent dispatch, anticipating the next invocation will be on the same
type? This
would be very helpful in loops.
fun0
Hi,
S4 method dispatch can be very slow. Would it be reasonable to cache the
most
recent dispatch, anticipating the next invocation will be on the same
type? This
would be very helpful in loops.
fun0 - function(x)
sapply(x, paste, collapse=+)
fun1 - function(x) {
paste -
Hi Vince,
Martin forwarded your message about allowing more control over the show
method. There are now 2 global options that control the number of lines
displayed in the head and tail:
showHeadLines
showTailLines
When set, these options affect GenomicRanges, GappedAlignments, Ranges
and
Hi Michael,
Thanks for reporting the bug and sending a reproducible example. Sorry
it took a few days to get to this.
A fix has been checked into versions 1.4.12 (release) and 1.5.44 (devel).
Valerie
On 03/07/13 05:43, Michael Stadler wrote:
Here is the second attachment (variants.vcf)
Hi Moritz,
Thanks for the bug report and suggested fix. The patch has been applied
to 1.4.10 in release and 1.5.42 in devel.
Valerie
On 03/05/2013 07:05 AM, Moritz Gerstung wrote:
Hi,
I discovered the following problem in the geno() elements of the VCF object
when I load multiple regions
Julian,
I'm trying to produce a vcf file with these premature endings for
testing but am having no luck. Can you send me a small example of a vcf
with the premature ends? Or maybe there is a combination of VEP flags
that often result in this case?
Thanks,
Valerie
On 02/26/13 09:50, Julian
Thanks for catching this. A fix is checked in to 0.99.13.
It's great to have a tester for this package. Let me know if you have
suggestions/feedback for the user interface, how the param options are
specified etc.
Valerie
On 02/27/13 07:25, Julian Gehring wrote:
Hi,
'VEPParam' allows to
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