graph-genome component_segmentation issues

graph-genome / component_segmentation

Read in ODGI Bin output and identify co-linear components

Apache License 2.0

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referenced dataclass is not found

#51 mr-c closed 3 years ago
5
Improvement: Don't let components Self-Segment

#50 josiahseaman opened 3 years ago
0
don't always exit 0, especially in case of OOM

#49 mr-c closed 4 years ago
1
CS might add links where none are given from `odgi bin`

#48 subwaystation opened 4 years ago
5
various optimizations

#47 dimatr closed 4 years ago
4
estimate for segmentation.py memory usage

#46 mr-c opened 4 years ago
3
v14 I43 prerender information

#45 josiahseaman closed 4 years ago
2
ontology repacking and exporting - relates to #34

#44 dimatr opened 4 years ago
38
v14: pre-render information in output files

#43 josiahseaman closed 4 years ago
0
Zooming: processing file input and bin2file JSON v13

#42 mandosoft closed 4 years ago
1
Find Annotation and Knowledge Graphs to integrate

#41 josiahseaman opened 4 years ago
10
Optimizations

#40 dimatr closed 4 years ago
3
WIP: ontology and the .ttl writer

#39 dimatr closed 4 years ago
3
improving memory usage, see #23

#38 dimatr closed 4 years ago
1
Bin ranges

#37 dimatr closed 4 years ago
8
Synchronize JSON schema with odgi

#36 subwaystation closed 4 years ago
1
Fixes #12 Zooming

#35 mandosoft closed 4 years ago
4
Turtle output

#34 subwaystation opened 4 years ago
5
parallel json parsing

#33 dimatr closed 4 years ago
7
Allow empty link arrays, fix links statistics

#32 lomereiter closed 4 years ago
0
segment_matrix improvements (#30)

#31 lomereiter closed 4 years ago
3
Refactor segment_matrix to use numpy/pandas data structures

#30 lomereiter closed 4 years ago
3
v15: Sparse JSON output

#29 lomereiter closed 3 years ago
2
Zooming: separate directories: Fixes#12 and adds to #16 v11 and v12

#28 mandosoft closed 4 years ago
3
improvements in find_dividers function (#20)

#27 lomereiter closed 4 years ago
2
#21: use binary search to make things faster in populate_component_ma…

#26 dimatr closed 4 years ago
3
evaluate Numba for speeding up tight loops

#25 subwaystation closed 3 years ago
1
write internal tests for each refactored element

#24 subwaystation opened 4 years ago
0
optimize memory consumption

#23 subwaystation opened 4 years ago
1
evaluate JSON libraries for parsing large ODGI bin files

#22 subwaystation opened 4 years ago
1
refactor populate_component_matrix (loop rearrangement / binary search where appropriate)

#21 subwaystation closed 4 years ago
3
refactor find_dividers (loop rearrangement / binary search where appropriate)

#20 subwaystation closed 4 years ago
4
Optimized Implementation by integrating with odgi

#19 josiahseaman opened 4 years ago
0
Fixes to #11 Chunking FASTA Files

#18 mandosoft closed 4 years ago
1
I13

#17 subwaystation closed 4 years ago
3
v11-16: bin2file.json format changes

#16 josiahseaman opened 4 years ago
0
Chunk ids are not consecutive.

#15 6br closed 4 years ago
7
v13: HaploBlocker Outputs available for Schematize

#14 josiahseaman opened 4 years ago
0
ModuleNotFoundError: No module named 'matrixcomponent'

#13 subwaystation closed 4 years ago
1
v12: Zooming: separate directory for each bin_width

#12 josiahseaman closed 4 years ago
4
v11: Chunk Fasta files in parallel with components

#11 josiahseaman closed 4 years ago
3
output folder + logfile handling

#10 joehagmann closed 4 years ago
0
this fixes i8

#9 subwaystation closed 4 years ago
0
Read bin_width from JSON instead of command line argument

#8 subwaystation closed 4 years ago
0
Split on Maximum Component Size

#7 josiahseaman closed 4 years ago
0
Change bin-size to bin-width so we have consistent naming across tools

#6 subwaystation closed 4 years ago
3
IndexError: list index out of range

#5 6br closed 4 years ago
9
Split files so Schematize does not crash

#4 subwaystation closed 4 years ago
25
Put coverage, inversion and position into JSON instead of Bool Vals for Occupation.

#3 subwaystation closed 4 years ago
2
Add data: Path occupancy per component

#2 josiahseaman closed 4 years ago
0