[BioC] readGappedAlignmentPairs with multimapping reads

[Vedran Franke [guest]]

How does the readGappedAlignmentPairs from the GenomicRanges library handle reads that map to several places in the genome?

Sometimes it can happen that one pair of the read is flagged as properly paired even if the other read maps to several locations, how is this handled?

Thank you in advance!

 -- output of sessionInfo(): 

R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
 [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
 [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
 [7] LC_PAPER=C                     LC_NAME=C
 [9] LC_ADDRESS=C                   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] GenomicRanges_1.8.3 IRanges_1.14.2      BiocGenerics_0.2.0
[4] plyr_1.6            stringr_0.6         BiocInstaller_1.4.4

loaded via a namespace (and not attached):
[1] stats4_2.15.0 tools_2.15.0


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