[R] ShortRead with BWA

[Duke]

Dear folks,

Please welcome a newbie both to R and the mailing list :). I am 
currently working on a sequencing project, and heard about R as well as 
some of its packages for next gen sequencing, and decided to give it a 
try. Starting with ShortRead, I found a document 
(http://www.bioconductor.org/packages/2.5/bioc/vignettes/ShortRead/inst/doc/ShortRead_and_HilbertVis.pdf) 
which does mention that readAligned was extended to support SAM format 
(for example, BWA output).

So I tried readAligned with

BWAAln <- readAligned(BWAFile, type = "BWA")

but then I got error:

 > BWAAln <- readAligned(BWAFile, type = "BWA")
Error: UserArgumentMismatch
   arugment 'type' had value 'BWA' allowable values: 'SolexaExport'
     'SolexaAlign' 'SolexaPrealign' 'SolexaRealign' 'SolexaResult'
     'MAQMap' 'MAQMapShort' 'MAQMapview' 'Bowtie' 'SOAP'

It looks like ShortRead does not support BWA. Am I right, or what am I 
doing wrong? Anybody has any idea?

Thanks,

D.