[Bioc-devel] GenomicAlignments: using asMates=TRUE and yieldSize with paired-end BAM files

[Michael Love]

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