[Bioc-sig-seq] extendRanges - error with AlignedRead vs GenomeData?

[Paul Leo]

I'm probably missing something here but AS follows demonstrates the problem:

> aln  ## have an ReadAligned object: has filtered and mapped data...
class: AlignedRead
length: 808363 reads; width: 36 cycles
chromosome: chr7.fa chr17.fa ... chrUn_random.fa chr6.fa 
position: 149076877 49506799 ... 5496653 88709067 
strand: - + ... - + 
alignQuality: NumericQuality 
alignData varLabels: run lane ... y filtering 

> aln.genome<-as(aln,"GenomeData") #Make a corresponding GenomeData
object

> from.aln<-extendReads(aln,seqLen=200)  ### run extendreads on the
ReadAligned
There were 50 or more warnings (use warnings() to see the first 50)
##PROBLEM???  seems to have worked in that from.aln contains data.

#################################################
> warnings()
Warning messages:
1: In s1[[ineg]] - seqLen + readLen :
  longer object length is not a multiple of shorter object length
2: In s1[[ineg]] + readLen :

############### not SURE WHAT THESE WARNINGS are about ####

from.aln.genome<-extendReads(aln.genome,seqLen=200)  ### no warnings if
use a GenomeData object


###############  also not sure what is happening here !!!!
> from.aln<-extendReads(aln,seqLen=200,strand=c("+"))
Error in s1[[ineg]] : attempt to select less than one element
> from.aln<-extendReads(aln,seqLen=200,strand="-")
Error in s1[[ipos]] : attempt to select less than one element



any insight appreciated!  I would like to go from AlignedRead to Rle or
RleList directly if possible.

> sessionInfo()
R version 2.10.0 Under development (unstable) (2009-05-24 r48603) 
x86_64-unknown-linux-gnu 

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

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

other attached packages:
[1] chipseq_0.1.19    ShortRead_1.3.5   lattice_0.17-25
BSgenome_1.13.3  
[5] Biostrings_2.13.9 IRanges_1.3.16   

loaded via a namespace (and not attached):
[1] Biobase_2.5.2 grid_2.10.0   hwriter_1.1   tools_2.10.0