Hervé Pagès | 30 Sep 06:51 2013

Re: Sorting a GAlignments object by QNAME

Hi Rubi,

'gal[order(seqnames(gal))]' will sort GAlignments object 'gal' by QNAME.

H.

On 09/29/2013 12:32 PM, rubi [guest] wrote:
>
> Is there a way to sort the records in a GAlignments object by the QNAME, as this object is created with the
readGAlignmentsFromBam function where the bam file and its corresponding index file must be sorted by
RNAME and POS.
>
> Unless I'm missing something the only way I see how can this be done is read the bam into a data.table and sort that.
>
>   -- 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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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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