On Thu, Feb 27, 2014 at 4:37 PM, chris warth <cswarth@gmail.com> wrote:

> 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.
>
>
GenomicAlignments is mostly a reorganization of pre-existing functionality.
You should be able to call coverage() directly on your GAlignments, or on
the BamFile itself, with full support for cigar strings. Also, it is
sufficient to call readGAlignments(), i.e., no need for "FromBam".


> 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
>
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