[BioC] CIGAR-aware coverage

[chris warth]

I would like to gather coverage data for gapped alignments.  I am
using readGAlignmentsFromBam() to read a GAlignments object,
converting to an IRanges object and calling IRanges::coverage() , but
that ignores CIGAR strings.

There appears to be a message to BIOC-devel on CIGAR-aware coverage
( https://www.mail-archive.com/bioc-devel@r-project.org/msg01460.html )
that suggests using the 'GenomicAlignments' package.

As far as I can tell that is only available under 2.14, the
development version of bioconductor,  which would also require running
R-devel.

Is there any way to get CIGAR-aware coverage under bioconductor 2.13?

Thanks in advance,

Chris Warth
Fred Hutchinson CRC

P.S. Not to distract from the above question, but I would also like
CIGAR-aware retrieval of alignments.   readGAlignmentsFromBam()
retrieves alignments whose gap completely spans the range I am
interested in.   I haven't found a way to exclude alignments that
don't have any actual base alignments overlapping the range I asked
for.

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

locale:
[1] C

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

other attached packages:
 [1] wavelets_0.3-0       vegan_2.0-10         lattice_0.20-24
 [4] permute_0.8-3        rtracklayer_1.21.14  Rsamtools_1.13.52
 [7] Biostrings_2.29.19   BiocInstaller_1.12.0 GenomicRanges_1.14.4
[10] XVector_0.1.4        IRanges_1.20.6       BiocGenerics_0.7.8

loaded via a namespace (and not attached):
[1] BSgenome_1.29.1 RCurl_1.95-4.1  XML_3.98-1.1    bitops_1.0-6
[5] compiler_3.0.2  grid_3.0.2      stats4_3.0.2    tools_3.0.2
[9] zlibbioc_1.7.0