superphy prairiedog issues

superphy / prairiedog

next-gen pangenome graphs for predictive genomics

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Dgraph

#106 kevinkle closed 5 years ago
11
See about pre-computing nodes

#105 kevinkle closed 5 years ago
3
Debug pyinstrument stalling on actual graph creation

#104 kevinkle closed 5 years ago
1
Create a Docker image

#103 kevinkle closed 5 years ago
5
See about using path structure to do a similar filter to scoary

#102 kevinkle opened 5 years ago
0
Core genome "plugin"

#101 kevinkle opened 5 years ago
0
Split additional functions into a "plugins" folder

#100 kevinkle opened 5 years ago
1
"Killed" on panther

#99 kevinkle opened 5 years ago
1
Move functions in Snakefile to a snake.py

#98 kevinkle opened 5 years ago
0
Call lemongraph setup.py from our setup.py

#97 kevinkle opened 5 years ago
0
Delete DGL support

#96 kevinkle closed 5 years ago
1
Provide a wrapper for pyinstrument.Profiler

#95 kevinkle closed 5 years ago
2
Switch to our own version of tox-base

#94 kevinkle closed 5 years ago
1
Switch to our own version of tox-base

#93 kevinkle closed 5 years ago
0
Switch to our own fork of docker image for tox

#92 kevinkle closed 5 years ago
1
Consider adding Node metadata

#91 kevinkle opened 5 years ago
1
Support for `nosync` option, and increase map size (#89)

#90 kevinkle closed 5 years ago
1
Support for `nosync` option, and increase map size

#89 kevinkle closed 5 years ago
1
Add check to DB map size before setting

#88 kevinkle opened 5 years ago
0
Investigate visualizations for graph

#87 kevinkle opened 5 years ago
0
Investigate how query time scales with graph size

#86 kevinkle opened 5 years ago
0
Support for pyinstrument and additional tests

#85 kevinkle closed 5 years ago
1
Re-add SubgraphRef and Snakemake tests, + integration with pyinstrument

#84 kevinkle closed 5 years ago
1
Check all values in a repeat

#83 kevinkle closed 5 years ago
0
Investigate different sizes for k

#82 kevinkle opened 5 years ago
0
Tag as 0.1.2

#81 kevinkle closed 5 years ago
0
Support repeats, increased graph size, and add filename/contig headers

#80 kevinkle closed 5 years ago
1
Embed sepearte filename and contig header props to edges

#79 kevinkle closed 5 years ago
1
Fixes code to account for repeats

#78 kevinkle closed 5 years ago
0
RecursionError: maximum recursion depth exceeded

#77 kevinkle opened 5 years ago
2
Test running in PyPy

#76 kevinkle closed 5 years ago
12
Fixes #70 through setting LemonGraph mapsize (#71)

#75 kevinkle closed 5 years ago
0
Test test_graph_connected_repeats_full_path() should fine 2 connecting edges

#74 kevinkle closed 5 years ago
1
Encode filename and header as edge props

#73 kevinkle closed 5 years ago
1
Add a test against repeats in graph

#72 kevinkle closed 5 years ago
1
Fixes #70 through setting LemonGraph mapsize

#71 kevinkle closed 5 years ago
1
python3: lib/lemongraph.c:622: _edge_index: Assertion `DB_SUCCESS == r' failed.

#70 kevinkle closed 5 years ago
4
Support graph queries via cli

#69 kevinkle closed 5 years ago
1
Fix use of `incr` by changing `value` of edges to `incr`

#68 kevinkle closed 5 years ago
1
python3: lib/lemongraph.c:641: _prop_index: Assertion `DB_SUCCESS == r' failed.

#67 kevinkle closed 5 years ago
3
Parallelize pangenome creation via multiple txns?

#66 kevinkle closed 5 years ago
1
Support queries via cli and change LGGraph.path() sig to also return …

#65 kevinkle closed 5 years ago
1
Pangenome graph creation optimizations

#64 kevinkle opened 5 years ago
9
Support queries via cli and change LGGraph.path() sig to also return meta

#63 kevinkle closed 5 years ago
2
Added support for path queries and function to join kmers (#61)

#62 kevinkle closed 5 years ago
1
Added support for path queries and function to join kmers

#61 kevinkle closed 5 years ago
0
Integration with lemongraph + support queries for connectivity of kmers

#60 kevinkle closed 5 years ago
1
Support checking in lemongraph if two kmers are connected on the same contig

#59 kevinkle closed 5 years ago
0
Develop

#58 kevinkle closed 5 years ago
1
Initial integration with lemongraph

#57 kevinkle closed 5 years ago
0

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