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Martinsos / edlib

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
http://martinsos.github.io/edlib
MIT License
514 stars 167 forks source link

Improve cigar format #28

Closed Martinsos closed 8 years ago

Martinsos commented 10 years ago

It is not a custom to start alignment path with insertions in cigar: I should replace them with soft clipping CIGAR operation (S) which can come at the start or end of read. Also, I shoud add support for standard cigar format.

Martinsos commented 10 years ago

I added support for standard cigar. I found in SAM article that S is used for SW for parts of query that are not part of solution, so I am not sure this is applicable for HW, I have to investigate this further.