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Made insertion motif optional, expanded valid insertion sequence check and added support for target site deletions #216

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ramonamerong wants to merge 1 commit into adamewing:master from ramonamerong:master

ramonamerong commented Dec 13, 2022

I had simulated mobile element insertions using BAMsurgeon for my project but encountered the following problems:

The insertion motif did not work as intended so I made it optional.
Any other nucleotide notation other than ACGT was not supported, so I added ambiguous nucleotides.
While target site duplications are supported, target site deletions are not as (they occur more rarely). Therefore I made target site deletions possible if you set the TSD length to a negative value (e.g. -9).

I made this push request as I think others could benefit from these changes.


          Made insertion motif optional, expanded valid insertion sequence chec…

…k and added support for target site deletions

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