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
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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