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 a
constraint.
When yieldSize is given, say 100, then 100 mates are returned. The algo
moves through the file until 100 records are successfully paired. These
100 are yielded to the user and the code picks up where it left off. A
related situation is the 'which' in a param. In this case you want the
mates in a particular range. The algo moves through the range and pairs
what it can. If it's left with unmated records it goes outside the range
looking for them. readGAlignmentsList() will return all records in this
range, mated or not. The metadata column of 'mate_status' indicates the
different groupings.
Valerie
Mike
On Wed, Mar 19, 2014 at 1:04 PM, Valerie Obenchain <voben...@fhcrc.org
<mailto:voben...@fhcrc.org>> wrote:
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=10000, asMates=TRUE)
Maybe set some specifications in a param:
param <- ScanBamParam(what = c("qname", "flag"))
Then call either readGAlignment* method that handles pairs:
readGAlignmentsList(bf, param=param)
readGAlignmentPairs(bf, param=param)
For summarizeOverlaps():
summarizeOverlaps(annotation, bf, param=param, singleEnd=FALSE)
We've considered removing the 'obeyQname' arg and documentation but
thought the concept may be useful in another application. I'll
revisit the summarizeOverlaps() documentation to make sure
'obeyQname' is downplayed and 'asMates' is encouraged.
Valerie
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=character(0), yieldSize=3, obeyQname=TRUE)
https://stat.ethz.ch/__pipermail/bioconductor/2013-__March/051490.html
<https://stat.ethz.ch/pipermail/bioconductor/2013-March/051490.html>
If I want to use GenomicAlignments::__readGAlignmentsList with
asMates=TRUE and respecting the yieldSize, what is the proper
construction? (in the end, I want to use summarizeOverlaps on
paired-end BAMs while respecting the yieldSize)
library(pasillaBamSubset)
fl <- sortBam(untreated3_chr4(), tempfile(), byQname=TRUE)
bf <- BamFile(fl, index=character(0), yieldSize=3,
obeyQname=TRUE, asMates=TRUE)
x <- readGAlignmentsList(bf)
Warning message:
In scanBam(bamfile, ..., param = param) :
'obeyQname=TRUE' ignored when 'asMates=TRUE'
Calls: readGAlignmentsList ... .matesFromBam ->
.load_bamcols_from_bamfile -> scanBam -> scanBam
I see in the man pages for summarizeOverlaps it has:
"In Bioconductor > 2.12 it is not
necessary to sort paired-end BAM files by ‘qname’. When
counting with ‘summarizeOverlaps’, setting ‘singleEnd=FALSE’
will trigger paired-end reading and counting."
but I don't see how this can respect the specified yieldSize,
because
readGAlignmentsList has to read in as many reads as necessary to
find
the mate.
Sorry in advance if I am missing something in the documentation!
Mike
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