Convex BiWFA for pureWFA and patching #197
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fix unset variable
Initialize stage2 scan flag
Output ANI in [0, 1] instead of [0, 100]
fix id representation
All outputs in [0, 1] now (again)
Average kmer complexities over chain in mergeMappingsInRange
add `guix.scm`
Enable one to one filtering
Add error when the index is empty
Don't include endpoint in L2 range
make the script more robust
Do not allow a segment to chain with itself
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Convex penalties allow better resolution of structural variants. We apply it only for patching, as it has a cost.
This replaces #145.