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Update distance index #163

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wants to merge 43 commits into from
Closed

Update distance index #163

wants to merge 43 commits into from

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xchang1
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@xchang1 xchang1 commented Aug 22, 2022

Make a bunch of changes to make the distance index faster and correct
Also rename the static get_net_handle for issue #160

xchang1 and others added 30 commits May 20, 2022 11:41
@xchang1
Add connected_component_count()
19c955a
@xchang1
Fix finding the length of a trivial chain
b91b14a
@xchang1
Update documentation
64637fc
@xchang1
Add space for paths through connected components but only chains
a567074
@xchang1
Add chain component to paths
6b6d917
@xchang1
Add slot to nodes to store path and offset, but only trivial chain no…
b395381 
…des in snarls
@xchang1
Store path values properly
0e0c24f
@xchang1
Save the connected component of the longest path, not the offset
c3e8e77
@xchang1
Take out debug output
0a8c5bb
Make sure that there are enough bits to represent path values
1f63759
Add traceback for distance but the last commit broke stuff
5ba2ae4
@xchang1
Make snarls with long traversals oversized snarls
5c40bd2
@xchang1
Merge remote-tracking branch 'origin/distance-index' into HEAD
a05c522
@xchang1
Get distance traceback properly
62ed1b5
@xchang1
Take out debug
cb8a17f
@xchang1
Fix traceback for single nodes
d8eadf6
@xchang1
Add traversal of shortest path
c666cd4
@xchang1
Fix bugs in shortest path traversal
2ee1b43
Don't visit boundary nodes twice
fbd57db
Fix traversals
8523f06
Fix orientations but not loops in chains
f9afe98
Try to add loops in chain paths but it doesn't work yet
215e520
Last commit still doesn't work but fixed loops in trivial chains
960f8b8
Stop duplicating looping traversals
3bf6a75
Fix looping from the same snarl in a chain
30daea5
Don't double up boundary node lengths
4efa061
Actually look for distance between the same node in a snarl
f68c8ce
Use libhandlegraph's minimum distance traversal in big snarls
f70dcd5
Fix traversal of root children
fd9e269
Add minimum distance path for nested chains
9491ee7
xchang1 and others added 13 commits July 26, 2022 17:28
@xchang1
Retraverse chain in snarl after looping
74fab0e
Don't use get_chain_component when the node matters
ceca349
Save the record offset instead of connected component for paths
0f4383d
Reverse node before checking if it's the end
a587f3d
Switch to using handlegraph::algorithms::for_each_handle_in_shortest_…
3586d8b 
…path because I don't know what's wrong with this one
Take the minimum distance path out of the index
9c9bfea
Move distances to bounds of parent into nodes and chains
1aae19a
Make get_distance_to_parent_bound use distances from child
718339b
Don't go to the records for is_root_snarl
9346e0f
Make sum take a reference to a vector
0dd9b2f
Use reduce to get sum
0fe1cb8
Use accumulate instead of reduce because the compiler can't find reduce
8d66da8
Rename static get_net_handle to appease ReadTheDocs
51533d9
@xchang1 xchang1 closed this Aug 22, 2022
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