[BioC] Obtain overlap coordinates in GenomicRanges findSpliceOverlaps

[rubi [guest]]

Hi,

I was wondering whether it is possible in anyway to obtain the overlap coordinates when intersecting GAlignments objects as query with a GRangesList object, using the findSpliceOverlaps function?

Specifically, I would like to obtain the transcriptomic coordinates of the GAlignments in the transcripts that they compatibly intersect with. 

Right now I'm obtaining this information in a 2 step approach:
1. findSpliceOverlaps(GAlignments, GRangesList, ignore.strand=FALSE)
2. Keeping only the hits that are compatible, I then intersect again each GAlignment and the ranges of the compatible GRange transcript and sum the widths of the exons up to the intersection coordinate.

My problem is that the second step is extremely slow.

I'd be grateful for some discussion

 -- output of sessionInfo(): 

R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] hash_2.2.6           data.table_1.8.10    Rsamtools_1.14.3
[4] Biostrings_2.30.1    GenomicRanges_1.14.4 XVector_0.2.0
[7] IRanges_1.20.6       BiocGenerics_0.8.0

loaded via a namespace (and not attached):
[1] bitops_1.0-6   stats4_3.0.2   tools_3.0.2    zlibbioc_1.8.0


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