[BioC] Rsamtools: scan all optional tags that exists in my bam file

[Martin Morgan]

On 09/28/2013 11:30 AM, rubi [guest] wrote:
>
> Hi,
>
> Using Rsamtools to read a bam file, is there a way to scan all the optional
> tag fields that exists in the bam file without having to explicitly specify
> them a priory in the ScanBamParam argument?

No, you've got to specify explicitly the tags you want; there's nothing in the 
BAM header specification that indicates the tags present in the file (otherwise 
scanBamHeader() might have helped) and there's no way to say 'give me each tag 
as it's encountered' in Rsamtools.

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
>
> -- Sent via the guest posting facility at bioconductor.org.
>
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