[BioC] Rsamtools: ScanBamParam IsUnmappedQuery flag

[Thomas Unterthiner]

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?)

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