Hi All

I want to extract the genomic locations of insertions and deletions of 
aligned reads. In the BAM file, I identify the insertions/deletions from 
the cigar string. However I would need to translate this cigar string 
into genomic coordinates.

 From reading the documentation, it seems that the method 
GenomicRanges::queryLoc2refLoc would be the suitable method. The 
documentation says:

> For|queryLoc2refLoc|: An integer vector of the same length 
> as|qloc|containing the "reference-based locations" (i.e. the 1-based 
> locations relative to the reference sequence) corresponding to the 
> "query-based locations" passed in|qloc|.
>
>
Unfortunately it is not yet implemented. Would there be another option 
or a workaround?

Best regards
Hubert


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