[BioC] Howto achieve reverse complement in a ShortReadQ object

[Tomas Bjorklund [guest]]

I have a set of data coming from a PacBio RSII circular consensus sequencing (CSS). In this dataset, the reads have a random orientation. For my further analysis, I require them to be reoriented to have the same orientation, but retain the phred quality information and ID, i.e., I need the final data to be in a ShortReadQ object.

I cannot find a function that achieves a reverse complement on the sequence and the reverse on the quality. Is there one that I'm missing?

for the reverse complement on the sequence I can conduct the following command:
myReads at sread <- reverseComplement(myReads at sread)

where "myReads" is the ShortReadQ object.

there is also a reverse command, but this is not available for the FastqQuality, i.e., 

myReads at quality <- reverse(myReads at quality)     does not work!

I have tried to generate a for loop but run into the issue that the FastqQuality object is not subsettable

I highly appreciate if someone could help me find a solution for this

All the best

Tomas




 -- output of sessionInfo(): 

R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ShortRead_1.22.0        GenomicAlignments_1.0.0 BSgenome_1.32.0         Rsamtools_1.16.0        GenomicRanges_1.16.2   
 [6] GenomeInfoDb_1.0.2      Biostrings_2.32.0       XVector_0.4.0           IRanges_1.22.3          BiocParallel_0.6.0     
[11] BiocGenerics_0.10.0    

loaded via a namespace (and not attached):
 [1] BatchJobs_1.2       BBmisc_1.6          Biobase_2.24.0      bitops_1.0-6        brew_1.0-6          codetools_0.2-8    
 [7] DBI_0.2-7           digest_0.6.4        fail_1.2            foreach_1.4.2       grid_3.1.0          hwriter_1.3        
[13] iterators_1.0.7     lattice_0.20-29     latticeExtra_0.6-26 plyr_1.8.1          RColorBrewer_1.0-5  Rcpp_0.11.1        
[19] RSQLite_0.11.4      sendmailR_1.1-2     stats4_3.1.0        stringr_0.6.2       tools_3.1.0         zlibbioc_1.10.0    

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