Using the -C option of damapper produces to two LAS files [B-reads].[A-reads].las and [A-reads].[B-reads].las. Currently, both files are used for different purposes and a mapping between alignment chains of both must be made. This seems to generate unnecessary complexity, thus opening doors for errors.
Tasks
[x] Why are both files being used?
[x] Refactor the whole code base as to avoid using both. A starting point is to remove djunctor.djunctor.AlignmentContainer.
Using the
-Coption ofdamapperproduces to two LAS files[B-reads].[A-reads].lasand[A-reads].[B-reads].las. Currently, both files are used for different purposes and a mapping between alignment chains of both must be made. This seems to generate unnecessary complexity, thus opening doors for errors.Tasks
djunctor.djunctor.AlignmentContainer.