[BioC] Rsamtools: ScanBamParam IsUnmappedQuery flag

[Martin Morgan]

On 07/19/2010 09:49 AM, Thomas Unterthiner wrote:
> Hi there!
> 
> According to the documentation, the "isUnmappedQuery" should be set to
> FALSE if I want to obtain only unmapped reads and to TRUE if I am only
> interested in mapped reads. However I find that it works exactly the
> other way around.
> 
> I.e. executing:
> 
> y <- scanBam(file, param=ScanBamParam(what=c("qname"),
>              flag=scanBamFlag(isUnmappedQuery=TRUE))))
> 
> and grepping for the returned query-names in the bamfile itself I find
> only reads that are not mapped, whereas changing the isUnmappedQuery to
> FALSE i get reads that indeed are mapped. This is exactly opposite to
> what the documentation states:
> 
> "isUnmappedQuery: A logical(1) indicating whether unmapped (FALSE),
>           mapped (TRUE), or any (NA) read should be returned."
> 
> 
> I am thus assuming there is a mistake in either the documentation or the
> code. Which one is it? (Or, am I just doing something wrong and not w/o
> it?)

It's a documentation error, should be fixed when 1.0.6 reaches
biocLite() in 24-36 hours. Thanks for the report. Martin

> 
> Cheers
> 
> Thomas
> 
> 
> ----------
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-pc-linux-gnu
> 
> locale:
>  [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>  [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
>  [7] LC_PAPER=en_US.utf8       LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] Rsamtools_1.0.5     Biostrings_2.16.6   GenomicRanges_1.0.5
> [4] IRanges_1.6.8
> 
> loaded via a namespace (and not attached):
> [1] Biobase_2.8.0
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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