Thanks a lot for all the advices - now it works! Great- If i may propose:
I couldn't find any information on the functions you used in the developer-doc's so i think it would be nice to mention in the documentation that:
- alignedReadStore's beginPos/endPos return gap space coordinates
- document the undocumented functions contigGaps() and positionGapToSeq()
- point out the differences if contig sequences are not available...
Thanks again for the excellent support!
All the best!