[BioC] Rsamtools: write a GAlignments object to a bam file

[Martin Morgan]

On 09/28/2013 12:44 PM, rubi [guest] wrote:
>
> Hi,
>
> I have a GAlignments object which I read from a bam file and have modified. I would like to write the modified GAlignments object now to a new bam file. I only came across the filterBam option in Rsamtools which I don't think will work. Is there any way to do this?
> If so, I would also like to be able to provide it with a header.

No, writing new or modified records is a big gap in the current Rsamtools; I 
know that the CRAN package rbamtools has write capabilities, but I have not used 
it and do not know how well / if it would play with Rsamtools (or perhaps its 
approach is sufficient for your purposes).

Martin

>
>   -- output of sessionInfo():
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] doParallel_1.0.3      iterators_1.0.6       foreach_1.4.1         data.table_1.8.10     Rsamtools_1.13.44     Biostrings_2.29.19    GenomicRanges_1.13.45 XVector_0.1.4
>   [9] IRanges_1.19.38       BiocGenerics_0.7.5
>
> loaded via a namespace (and not attached):
> [1] bitops_1.0-6    codetools_0.2-8 stats4_3.0.2    tools_3.0.2     zlibbioc_1.7.0
>
> --
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>
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