tweak output format for multipatch

Merge pull request #257 from waveygang/mm-index-only

allow only creating the index and exiting

add biwfa citation

Merge pull request #242 from waveygang/specify-queries

Specify queries

Merge pull request #238 from waveygang/dynamic_chain_gap

for the chain_gap, do not go above 20k by default

Merge pull request #229 from waveygang/convex_patching

Convex penalties for the alignment patching

Merge pull request #222 from waveygang/split_approx_robust

make the script more robust

version v0.12.5

update nix build... again

version v0.12.4