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 wrote:
>
>
> On Wed, Mar 19, 2014 at 4:26 PM, Valerie Obenchain wrote:
>
>> Thanks for the feedback.
>>
>> I'll look into nchar for XStringSetList.
>>
>>
On Wed, Mar 19, 2014 at 4:26 PM, Valerie Obenchain wrote:
> Thanks for the feedback.
>
> I'll look into nchar for XStringSetList.
>
> I'm in favor of supporting isDeletion(), isInsertion(), isIndel() and
> isSNV() for the VCF classes and removing restrictToSNV(). I could add an
> argument 'all_alt
Thanks for the feedback.
I'll look into nchar for XStringSetList.
I'm in favor of supporting isDeletion(), isInsertion(), isIndel() and
isSNV() for the VCF classes and removing restrictToSNV(). I could add an
argument 'all_alt' or 'all_alt_agreement' to be used with CollapsedVCF
in the case w
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
wrote:
>
>
>
> On Wed, Mar 19, 2014 at 4:00 PM, Michael Lawrence <
> lawrence.mich...@gene.com> wrote:
>
>> It would be nice to have funct
On Wed, Mar 19, 2014 at 4:00 PM, Michael Lawrence 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 ExpandedVCF.
>
> Also, it w
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 wrot
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 ExpandedVCF.
Also, it would be nice if restrictToSNV just assumed that alt(x) must be
somet
I would say rows 1 and 3 are SNVs, but not row 4. For this application
I think a variant has to be an SNV or not, as you can't pass half a
variant. (I suppose you could remove the ALT values with length > 1 and
set those genotypes to missing, but that is both complicated and
unexpected behavi
On 03/19/14 10:24, Michael Love wrote:
hi Valerie,
If the Bam is not sorted by name, isn't it possible that readGAlignment*
will load > yieldSize number of reads in order to find the mate?
Sorry, our emails keep criss-crossing.
Because the mate-pairing is now done in C yieldSize is no longer
Hi Mike,
You no longer need to sort Bam files to use the pairing algo or
yieldSize. The readGAlignment* functions now work with both constraints
out of the box.
Create a BamFile with yieldSize and indicate you want mates.
bf <- BamFile(fl, yieldSize=1, asMates=TRUE)
Maybe set some specif
On 03/19/14 07:39, Michael Love wrote:
hi,
From last year, in order to use yieldSize with paired-end BAMs, I
should sort the BAMs by qname and then use the following call to
BamFile:
library(pasillaBamSubset)
fl <- sortBam(untreated3_chr4(), tempfile(), byQname=TRUE)
bf <- BamFile(fl, index=c
hi Valerie,
If the Bam is not sorted by name, isn't it possible that readGAlignment*
will load > yieldSize number of reads in order to find the mate?
Mike
On Wed, Mar 19, 2014 at 1:04 PM, Valerie Obenchain wrote:
> Hi Mike,
>
> You no longer need to sort Bam files to use the pairing algo or yi
hi,
>From last year, in order to use yieldSize with paired-end BAMs, I
should sort the BAMs by qname and then use the following call to
BamFile:
library(pasillaBamSubset)
fl <- sortBam(untreated3_chr4(), tempfile(), byQname=TRUE)
bf <- BamFile(fl, index=character(0), yieldSize=3, obeyQname=TRUE)
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