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/).
Than
tion to my 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 <mailto:voben...
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 a
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 deleted]
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 on
Val's out today and I'm at least part of the problem so...
On 06/17/2014 10:13 AM, Michael Lawrence wrote:
On Tue, Jun 17, 2014 at 7:00 AM, Valerie Obenchain
mailto:voben...@fhcrc.org>>
wrote:
Hi Michael, Ryan,
Yes, it would be
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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, Herve):
Anyone have an itch for optimization? The writeVcf function is currently a
bottleneck in our
ut I think
that either the preprocess.reads function should be required to only
take one argument, or else the method of passing through additional
arguments to it should be documented.
-Ryan
On Tue 05 Aug 2014 05:12:41 PM PDT, Ryan C. Thompson wrote:
Hi Valerie,
I got really busy around May and neve
all to
summarizeOverlaps. These actually get passed straight to
preprocess.reads. Perhaps the documentaion 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&#x
d by a dedicated writer
process?).
Thanks,
Jeff
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Fred H
apply()
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 fo
5, 2014 at 2:33 PM, Valerie Obenchain 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:
tring
manipulation in writeVcf. We either need 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,
ows and the improvement over writeVcf() in release is ~ 90%.
Valerie
On 09/04/14 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
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 Obencha
be
rtracklayer).
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
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'
imenting with this. You
can override default chunking with 'nchunk'. Examples on the man page.
Valerie
On 09/08/14 08:43, 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...@fhcr
Just a note to say thanks to those who worked on (1) the new biocViews
search capabilities and (2) seqlevelsStyle<-. These are great
improvements that have made tasks easier / faster time and time again.
Yea!
Val
___
Bioc-devel@r-project.org mailing
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 w
me know if you need more details, I can send another 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
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 '
rjson_0.2.14
[31] RSQLite_0.11.4 sendmailR_1.2-1
[33] splines_3.1.1 stringr_0.6.2
[35] survival_2.37-7tools_3.1.1
[37] 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, V
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 al
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 mai
Hi Robert,
Annotation packages are generally updated before each release. You
should have received an email from Marc (cc'd) last month asking if you
had any updates. Updated packages are uploaded to our ftp server and
Marc adds them to the repository.
If you need to make a change I think Ma
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 th
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 Obenchain wrote:
Hi Robert,
Thanks for the bug report and reproducible example. Now fixed in release
1.12.2 and d
s over chunks of GRanges. Within your MAP
function:
import(file, which = ranges, as = "Rle", format = "bw")[ranges]
returns an RleList, and calling mean() on this gives a numeric vector
of the mean of the coverage for each range.
Then the only work needed is how to package t
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
MA
r a subset of cells in the (ranges, files) matrix, and
asking/estimating the amount of memory available for each worker.
best,
Mike
On Mon, Oct 27, 2014 at 2:35 PM, Valerie Obenchain mailto:voben...@fhcrc.org>> wrote:
Hi Kasper and Mike,
I've added 2 new functions to Genomi
nges
element. In other words, VCF 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
mailto:voben...@fredhutch.org>> wrote:
This could be fixed in the VRanges -> VCF coercion or in
was just being too helpful, 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
mailto:voben...@f
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
wrote:
Hi,
The conversion fro
Now in IRanges 2.0.1 and VariantAnnotation 1.12.7.
Valerie
On 12/11/2014 09:32 AM, Julian Gehring wrote:
Can you backport the fixes to bioc-release which is also affected?
Best
Julian
Valerie Obenchain (12/09/14 03:24):
Thanks to Michael and Julian for taking care of this. Fixes are in
Hi Sean,
Yes, we are aware of the problem, thanks. Hopefully this will be
resolved for tomorrows builds ... we'll post back when it's fixed.
Val
On 12/14/2014 08:33 AM, Sean Davis wrote:
Hi, Martin, Val, and Herve.
This looks like a little problem with the bitnames in
Rsamtools/GenomicAlign
gGraphs/inst/scripts/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
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 of
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 c
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 varian
s.
cheers,
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 t
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 an
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
row.n
Hi Mike,
Our error - we didn't bump GenomicRanges when rowRanges was added.
Hopefully 1.19.43 will propagate today and things will be sorted out.
Val
On 03/06/2015 07:40 AM, Michael Love wrote:
hi all,
just a practical issue: I have GenomicRanges version 1.19.42 on my
computer which does n
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 erro
traint.
Changes are in 1.19.46.
Valerie
On 03/06/2015 08:20 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
Hi Leo,
Thanks for reporting this. It was missed by the build system (and
myself!) because the package was already installed. Should be fixed in
1.1.16.
futile.logger (and others) were moved to Suggests to lighten the load of
the NAMESPACE. Logging isn't technically turned on until the clust
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
t
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 mailto:robert.cast...@upf.edu>> wrote:
+1 IMO BioC could adopt the zero-width ranges representation for
insertions, adapting readVcf(), writeVcf()
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,
D annotations that i described below the bug, between
predictCoding() and locateVariants()?
robert.
Original message ----
From: Valerie Obenchain
Date:17/03/2015 19:18 (GMT+01:00)
To: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] little tiny bug in CDSID annotations from
predic
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 mailto:robert.cast...@upf.edu>> wrote:
+1 IMO BioC could adopt the zero-width ranges representation for
insertions, adapting readVcf(), writeVcf()
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Hi Leo,
Thanks for reporting the bug with import. The problem was in how the
length of the output was computed. This has been fixed in both release
(1.28.3) and devel (1.29.6).
I'll let Michael answer the summary() question.
Valerie
On 05/19/2015 12:10 PM, Leonardo Collado Torres wrote:
H
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
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.
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,
currently, the annotation of variants in intronic regions by
VariantAnnotation and the locateVariants() function does not assign
strand to annotations in intron
enomicAlignments_1.4.1 BiocParallel_1.2.2
BSgenome_1.36.0
[5] tools_3.2.0 DBI_0.3.1 lambda.r_1.1.7
futile.logger_1.4.1
[9] rtracklayer_1.28.4 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-
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
sn't suggesting that LOCSTRAND be added to the locateVariants()
output. Rather, it would be added to the VRanges during the merge.
Michael
On Thu, Jun 11, 2015 at 10:10 AM, Valerie Obenchain
wrote:
locateVariants(), predictCoding() and the family of mapToTranscripts()
functions all retur
July newsletter available at
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Hi Leo,
Thanks for the sample code I'll take a look.
You're right, SnowParam has changed quite at bit - logging, error
handling etc. The memory use you're seeing is a concern - thanks for
reporting it.
As an fyi, the log output for SnowParam and MulticoreParam now includes
gc(), system.time
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 abst
/vignettes/BiocParallel/inst/doc/Errors_Logs_And_Debugging.pdf
there's a typo. It reads "SnowParma" instead of "SnowParam".
Thanks, I'll fix that.
Valerie
On Fri, May 22, 2015 at 5:33 PM, Valerie Obenchain
wrote:
Hi,
Thanks for reporting the bug. Now fixed in 1.13.4
as well as compare cluster environments.
However, the gc() numbers from R 3.1.x (only available on the 4th
replicate run) 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
wrote:
Hi Leo,
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
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 liberal
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:
No
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. Consider
Hi Robert,
I will look into this next week. Thanks for providing details and
examples in the request.
Valerie
On 02/06/2013 04:10 PM, Robert Castelo wrote:
dear maintainers of the graph package,
i have a small request for the constructor function graphBAM() from the
graph package.
the curr
ode(), which calls graphBAM(),
was returning unsorted node names. To remain consistent with previous
behavior I've sorted these results. Currently addNode() has no way to
specify a full list of node names. Do you have an opinion on addNode()
behavior? OK as is?
Valerie
On 02/07/20
Hi Julian,
Thanks for the bug report. I agree this situation should be handled. It
might be tomorrow before I get to this - I'll post back when it is done.
Valerie
On 02/26/2013 10:23 AM, Julian Gehring wrote:
Hi Richard,
That is true that is not according to the specs. However, the
'ensem
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 s
minimal VCF file and code to reproduce this via
e-mail. If you need more, please let me know.
Best wishes
Julian
On 02/27/2013 08:53 PM, Valerie Obenchain wrote:
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
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
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") t
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 XS
Hi Vince, Kasper,
cc'ing Herve and Marc.
I think we have a couple of things going on so I wanted to clarify. The
'genome' argument to readVcf() is assigned to the GRanges in rowData
with the "genome<-" setter. This is where .normargGenome() gets called.
setReplaceMethod("genome", "Seqinfo",
Hi Hector, Michael,
This sounds great. Bringing these into svn is fine with us. Michael, do
you want to merge these in?
Val
On 05/24/2013 07:30 AM, Hector Corrada Bravo wrote:
Thanks Michael,
It has made significant difference for our visualization project. I would
like to merge this into s
Hi all,
keepSeqlevels(), dropSeqlevels(), renameSeqlevels() and the new
restoreSeqlevels() are in GenomicRanges 1.13.16.
Major changes:
- These are high-level functions that wrap seqlevels(), not generics
with methods.
- All except restoreSeqlevels accept a named or unnamed character vecto
Hi Robert,
Have you seen TabixFile and TabixFileList? Both scanVcf() and readVcf()
have methods for TabixFile.
> showMethods("readVcf")
Function: readVcf (package VariantAnnotation)
file="character", genome="character", param="missing"
file="character", genome="character", param="ScanVcfParam"
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 GenomicFea
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
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, Val
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 implemented
lerie
On 08/23/2013 11:17 AM, Michael Lawrence wrote:
On Fri, Aug 23, 2013 at 8:41 AM, Valerie Obenchain 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
Hi,
On 09/04/2013 04:23 PM, Michael Lawrence wrote:
Hi, Val,
I just fixed expand,VCF to support multiple 'A' columns in info. Looks like
expand,DataFrame does a cartesian product of list columns, which is not
what we want in that case.
Thanks.
Ran up against another hurdle though: the conv
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
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 trying
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
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 and
-’ for signature
‘"VCFHeader", "SimpleDataFrameList"’
Do you think that you 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 br
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. 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
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 an
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 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.
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