new option '--idxPos0' (default=1) to guide indexing

[martin-raden]

• defines the in/out index of the first sequence position
• if negative; ignore 0 from indexing
• use this information to map mutation encoding to sequence position

(similar to IntaRNA --t/qIdxPos0)

• allows to study same mutation (encoding) within different sequence context lengths

[mmiladi]

I didn't get the idea..

[martin-raden]

right now, indexing always starts with 1. but mRNAs are usually indexed by the first position of the start codon. all indices upstream of the start codon are numbered negatively (skipping 0).

all you need for proper indexing supportign this scenario is to know what is the index of the first sequence position (idxPos0). thus, you need to map all input/output indices to internal 0-based indexing, best via two respective functions. that way, you can change sequence context length of an RNA around a mutation without changing the mutation index (by setting respective idxPos0 values).

That's quite useful if you want to provide figures/results for mRNAs that can be directly used afterwards without reindexing..

better explained? ;)

[mmiladi]

Thanks :-)