Hi Hervé and thanks for the response.

I assume you meant 'gal[order(names(gal))]' rather than
'gal[order(seqnames(gal))]'
in order to sort by QNAME (i.e. read ID)?

Using this, however, doesn't seem to sort gal by the same sorting rules
that sortBam or samtools sort -n does. Am I missing something?

Thanks,
rubi



On Mon, Sep 30, 2013 at 12:51 AM, Hervé Pagès <hpages@fhcrc.org> wrote:

> 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
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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