[BioC] Sorting a GAlignments object by QNAME

[Martin Morgan]

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.

Unsorted / sorted by qname files can be read in; likely the part that is 
tripping you up is the need to specify character() for index, perhaps with 
yieldSize and obeyQname

   bf = open(BamFile(fl, character(), yieldSize=1000000, obeyQname=TRUE))

If fl were sorted by qname (?sortBam, byQname=TRUE) then this would guarantee 
1000000 qnames per chunk

     repeat {
         aln = readGAlignmentsFromBam(bf)
         if (length(aln) == 0)
            break
         ## do work
     }

Since you've got the devel version, see also ?readGAlignmentsListFromBam which 
will read in mated reads from an RNAME,POS supported file in an iteration like 
above, with more modest memory requirements than reading in the entire file.

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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