Merge master into dev branch. #1
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Simplification was removing deletions at the beginning of mappings. This caused problems in merged alignments produced by banding, which generate multiple mappings to the same node.
Due to banding, multiple passes may be required to include paths. This should be parameterized, but for now I'm just testing.
These can handle multiple mappings per path.
Whoops, there was a bug with the last commit.
Hard to describe aside from "fixing bugs related to normalization of complex paths over graphs". I'm a bit closer to supporting paths in unchop.
This can take a mapping and split it into two mappings at a specified cut point, then store these in the paths. The rank that they are assigned is each the same as the original element, so only via normalization are the ranks going to be made correct.
Including cyclic paths in graphs
This ensures that normalization works as expected. These requirements for sibling set membership were heavy-handed and appear unnecessary in any of the tests I have available (stock test and HLA genes).
Add .pre-build make dependencies and deconstructor skeleton classes.
Conflicts: src/vg.cpp
… as otherwise it would take forever to push out nanopore reads.
…o that it may be sourced from anywhere. Also moved alignment output back to a 1000 alignment buffer
…banded alignments.
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Enough said, really. I've been in the bad habit of developing on master.