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superphy
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prairiedog
next-gen pangenome graphs for predictive genomics
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Working implementation of incremental edge ids
#56
kevinkle
closed
5 years ago
0
Lemongraph inc deb
#55
kevinkle
closed
5 years ago
0
Merge current integration with diffpool
#54
kevinkle
closed
5 years ago
0
pangenome graph creation
#53
kevinkle
closed
5 years ago
7
label graphs via prairiedog as req by diffpool
#52
kevinkle
closed
5 years ago
13
switch diffpool/GraphSampler to load on __getitem__()
#51
kevinkle
closed
5 years ago
1
Use Node Label for Kmer ID
#50
kevinkle
closed
5 years ago
1
IndexError: list index out of range
#49
kevinkle
closed
5 years ago
1
Running prairiedog for diffpool
#48
kevinkle
closed
5 years ago
4
ValueError: invalid literal for int() with base 10: '1 2'
#47
kevinkle
closed
5 years ago
1
switch node labels to node features (node attributes)
#46
kevinkle
opened
5 years ago
1
run diffpool with an mmap of subgraphs?
#45
kevinkle
closed
5 years ago
2
MemoryError with diffpool itegration
#44
kevinkle
closed
5 years ago
3
Update readme to use -j
#43
kevinkle
closed
5 years ago
1
Building PyTorch on panther
#42
kevinkle
closed
5 years ago
1
Set ver to 0.1.1
#41
kevinkle
closed
5 years ago
1
More log outputs (#39)
#40
kevinkle
closed
5 years ago
1
More log outputs
#39
kevinkle
closed
5 years ago
0
Split GraphRef into two parts: 1 for graphing new genomes, and one for training diffpool
#38
kevinkle
closed
5 years ago
1
Switch to Snakemake as task runner (#36)
#37
kevinkle
closed
5 years ago
1
Switch to Snakemake as task runner
#36
kevinkle
closed
5 years ago
1
Check IDs start at 1 (#34)
#35
kevinkle
closed
5 years ago
1
Check IDs start at 1
#34
kevinkle
closed
5 years ago
1
Cli (#32)
#33
kevinkle
closed
5 years ago
0
Cli
#32
kevinkle
closed
5 years ago
0
Have to graph Kmers as they are parsed or we run out of ram
#31
kevinkle
closed
5 years ago
1
Add option to set number of cores via cli
#30
kevinkle
closed
5 years ago
2
Creates all required files except the node_labels (#28)
#29
kevinkle
closed
5 years ago
1
Creates all required files except the node_labels
#28
kevinkle
closed
5 years ago
1
Fix dictionary mapping output
#27
kevinkle
closed
5 years ago
1
Ref kmer to some label by lookup and tag node
#26
kevinkle
closed
5 years ago
2
Tag nodes against kmer as attribute
#25
kevinkle
closed
5 years ago
1
Framework for creating required graph outputs + codecov integration
#24
kevinkle
closed
5 years ago
1
Support codecov.io
#23
kevinkle
closed
5 years ago
1
Check that the # of unique kmers == # nodes
#22
kevinkle
closed
5 years ago
0
Restructure code to support DiffPool format
#21
kevinkle
closed
5 years ago
0
Consider using offset + i E 2^k for node_ids
#20
kevinkle
closed
5 years ago
1
Tag graphs against MIC
#19
kevinkle
closed
5 years ago
1
Include memory profiling in tox (#17)
#18
kevinkle
closed
5 years ago
0
Include memory profiling in tox
#17
kevinkle
closed
5 years ago
0
create more detailed timing data for graphing
#16
kevinkle
closed
5 years ago
1
Basic setup for loading all kmers into a graph (#14)
#15
kevinkle
closed
5 years ago
0
Basic setup for loading all kmers into a graph
#14
kevinkle
closed
5 years ago
0
Basic setup for creating generic graphs
#13
kevinkle
closed
5 years ago
0
Basic setup for creating generic graphs
#12
kevinkle
closed
5 years ago
0
Add colored logs
#11
kevinkle
closed
5 years ago
0
Port of kmers done
#10
kevinkle
closed
5 years ago
0
Port of kmers done
#9
kevinkle
closed
5 years ago
0
Drop PyPy support due to slow file reads
#8
kevinkle
closed
5 years ago
0
Initial load of file
#7
kevinkle
closed
5 years ago
0
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