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A sampled step index implementation of the PG-SGD algorithm #454

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A sampled step index implementation of the PG-SGD algorithm #454

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@subwaystation subwaystation commented Oct 17, 2022 •
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  • Clean existing functionality.
  • Extensive refactoring.
  • Skeleton.
  • RISE.
  • Run along the path.
  • Fix ZIPF parts.
  • Functional odgi sort tests.
  • Performance tests. Compare with XP.
  • Functional odgi flip tests.
  • Functional odgi groom tests.
  • Functional odgi tips tests.
  • Functional odgi untangle tests.
  • ...

@subwaystation subwaystation changed the title A sampled step index implementation for the PG-SGD algorithm A sampled step index implementation of the PG-SGD algorithm Oct 17, 2022
@subwaystation
restructering
c00d7f3
@subwaystation
forgetti spaghetti
7e388e6
@subwaystation
refactory
9a9aa7b
@subwaystation
missing EOL
b763c10
@subwaystation
fix the FIXMEs is the plan
4659799
@subwaystation
re-volt
4b5f889
@subwaystation
Merge branch 'master' into pg_sgd_ssi
4efce0f
@subwaystation
SSI is the default route now
35f09b1
@subwaystation
Merge branch 'pg_sgd_ssi' of github.com:pangenome/odgi into pg_sgd_ssi
1804cd2
@subwaystation
we can clean the ssi
3575a2e
@subwaystation
CLEANERS
2b7896a
@subwaystation
ugly skeletor
3fbd887
@subwaystation
CMAKER
985f132
@subwaystation
node-step-bit-vector initialized
8e27d5c
@subwaystation
ns_bv in place
af6db6f
@subwaystation
bug fix
cf9631a
@subwaystation
happy
fad31c7
@subwaystation
pos of 1st step is retrieved via ssi!
588800c
@subwaystation
pos of 2nd step via ssi when we do uniform sampling
aea0b91
@subwaystation
some more tweaks
e583885
@subwaystation
hmm
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@subwaystation
working somehow
2cd5023
@subwaystation
cleanup
7e192b3
@subwaystation
playing around
c824efe
@subwaystation
better mirror initial implementation
7327513
@subwaystation
cleanup path_linear_sgd_schedule
b675cad
@subwaystation
refactor prepare_weak_connected_components_map
91c9f34
@subwaystation
refactor generate_and_write_snapshot_graphs
925683a
subwaystation
subwaystation commented Nov 7, 2022
View reviewed changes
src/algorithms/pg_sgd/path_sgd_ssi.cpp
step_handle_t cur_step;
cur_step = graph.path_begin(path);
bool lost = true;
// has_next_step is very, very costly and already unfeasable for yeast!
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:)

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