[Bioc-devel] accessing gapped alignment

[Daniel.Berner at unibas.ch]

dear developers
I have performed a gapped alignment of my illumina reads. I now want  
to analyze the output by accessing the CHROMOSOME and POSITION  
information contained in the BAM file. I therefore uploaded the BAM  
using readAligned(), but found that
all those reads aligning to the reference genome with a GAP are  
missing. However, when using readGappedAlignments(), I loose  
information crucial to my analysis (i.e., chromosome, position). Is  
there any way to upload into R GAPPED
alignments while preserving read ID, chromosome, position etc?
thanks,
Daniel Berner