hi all, we are faced with the problem of representing heterozygous indels in diploid resequenced data. normal heterozygotes (SNPs) in a diploid sequence can be represented with the various ambiquity symbols, but in my cursory look at the symbol/alphabet stuff in the biojava API docs, i did not see any way of representing ambiquities of the form: A/-, C/-, G/-, or T/- ... which are the four forms of a single base heterozygous indel in diploid data. is somebody working on this, and if not, does someone have suggestion about how to add this to the whole alphabet/symbol scheme of biojava? i am a relative novice at biojava; so if i have to implement this, i might need a little guidance to make sure that it is implemented in the correct way. doug
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