[BioC] Reading Paired End Native Report Format in ShortRead

[Murli Nair [guest]]

Hi,

I am trying to read the alignments generated using NovoAlign. The format I have the data is Paired End Native Report Format(http://computing.bio.cam.ac.uk/local/doc/NovoCraftV2.06.pdf). 
What is the most efficient way to read this data into ShortRead? Since it is paired end data I have two files corresponding to the two sides. 
I tried without success using the different formats using readAligned(). I also read an earlier posting about it which suggests to convert it to SAM format. 
I would appreciate your suggestions. 
Cheers../Murli


 -- output of sessionInfo(): 

R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] ShortRead_1.14.4    latticeExtra_0.6-19 RColorBrewer_1.0-5 
[4] Rsamtools_1.8.5     lattice_0.20-6      Biostrings_2.24.1  
[7] GenomicRanges_1.8.7 IRanges_1.14.4      BiocGenerics_0.2.0 

loaded via a namespace (and not attached):
[1] Biobase_2.16.0 bitops_1.0-4.1 grid_2.15.0    hwriter_1.3    stats4_2.15.0 
[6] tools_2.15.0   zlibbioc_1.2.0

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