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

Valerie Obenchain 
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:

Thread (8 messages)

Valerie Obenchain GenomicAlignments: using asMates=TRUE and yieldSize with paired-end BAM files Mar 19 Michael Love GenomicAlignments: using asMates=TRUE and yieldSize with paired-end BAM files Mar 19 Valerie Obenchain GenomicAlignments: using asMates=TRUE and yieldSize with paired-end BAM files Mar 19 Michael Love GenomicAlignments: using asMates=TRUE and yieldSize with paired-end BAM files Mar 21 Valerie Obenchain GenomicAlignments: using asMates=TRUE and yieldSize with paired-end BAM files Mar 27 Valerie Obenchain GenomicAlignments: using asMates=TRUE and yieldSize with paired-end BAM files Mar 27 Hervé Pagès GenomicAlignments: using asMates=TRUE and yieldSize with paired-end BAM files Mar 27 Valerie Obenchain GenomicAlignments: using asMates=TRUE and yieldSize with paired-end BAM files Mar 28