[BioC] Sorting a GAlignments object by QNAME

[rubi [guest]]

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

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