[BioC] readAligned with bowtie2 input

[Maria Dermit]

Dear list,

I am trying to read with some aligmnets files generated wiht Bowtie2 with
readAligned function of ShortRead package with this code:

readAligned("SRR030012.sra.1.aln.short.aln",type="Bowtie")

and I get this error:

error: unable to find an inherited method for function "strand", for
signature "AlignedRead"

I attach here the first 10 lines of one of my alignment files.

Many thanks for your help.

Kind Regards,

Maria

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

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

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

other attached packages:
[1] ShortRead_1.12.4     latticeExtra_0.6-24  RColorBrewer_1.0-5
[4] Rsamtools_1.9.30     lattice_0.20-10      Biostrings_2.25.12
[7] GenomicRanges_1.9.59 IRanges_1.15.42      BiocGenerics_0.3.1

loaded via a namespace (and not attached):
 [1] Biobase_2.14.0      bitops_1.0-4.1      BSgenome_1.25.7
 [4] grid_2.15.0         hwriter_1.3         RCurl_1.95-1.1
 [7] rtracklayer_1.17.19 stats4_2.15.0       tools_2.15.0
[10] XML_3.95-0.1        zlibbioc_1.4.0