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Merge SpLitteR #1366

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Merge SpLitteR #1366

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Itolstoganov
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  • Barcode index structure
  • Contracted graph structure
  • Scaffold graph vertices can store either edges or paths
  • SpLitteR tool

asl and others added 30 commits April 29, 2024 19:16
@asl
Some small include cleanup
d5ce5d4
@asl @Itolstoganov
Add example gfa splitter
a83a25f
@asl @Itolstoganov
Split GFA paths as well
005ebb7
@asl @Itolstoganov
Switch to new GFA parser
533ac5e
@Itolstoganov
Add link info to vertices. Fix graph reading
055bd0c
@asl @Itolstoganov
Split GFA paths as well
5bdf83c
@Itolstoganov
Initial commit
53bb961 
Added trivial resolver and barcode mapper fixes

Moved barcode mapper to graph pack

barcode mapper fix
@Itolstoganov
Added serialization
73cd059
@Itolstoganov
Changed main data structure to pair of separate maps for head and tai…
ee3a22e 
…l of the edge
@Itolstoganov
Added visualization
a88e3b7
@Itolstoganov
Changed barcode mapper structure
b3aacb3
@Itolstoganov
Changed BarcodeMapper structure
f65b655
@Itolstoganov
Find following edges via dijkstra
3454721
@Itolstoganov
Changed barcode score. Added path scaffolder. Paired-end stages
ad66757
@Itolstoganov
Added relative threshold to extension chooser
6d5829a
@Itolstoganov
Io refactoring
3b3aee8
@Itolstoganov
Changed coverage checks in PathJoiner
96c2d69
@Itolstoganov
Changed high coverage threshold (meaningless commit)
e5ed92c
@Itolstoganov
Made changes according to the newest version
0a4669e
@Itolstoganov
Added threshold on relative barcode coverage
2b8815b
@Itolstoganov
Barcode threshold now depends on gap length
e40248c
@Itolstoganov
Basic 10X support. BarcodeMapper refactoring
5893ae0
@Itolstoganov
Added 10X statistics
0ca8890
@Itolstoganov
Merged rr into general pipeline
28d117f
@Itolstoganov
Added backward check in read cloud resolver
3cffa98
@Itolstoganov
Separated storage from info extraction in BarcodeIndex. Various filters
b5bc3c1
@AntonBankevich @Itolstoganov
added new type of library: Clouds10x and new spades.py parameter --ge…
512d4f8 
…mcode1-1, --gemcode1-2
@Itolstoganov
Documentation stub. Added method that allows to get reliable barcode …
37b211e 
…intersection of two edges. Clouds10x libraries now have the same rights as PairedEnd
@Itolstoganov
Moved statistics into separate project
13ed588
@Itolstoganov
Removed gap closer optimization cutoff. Fixed online_vis. Added separ…
492de69 
…ate unique storage for read cloud resolver
Itolstoganov and others added 29 commits July 22, 2024 15:57
@Itolstoganov
Check if linked-read links are supported by the graph
c32d1cc
@Itolstoganov
Split partially resolved vertices
201dfb9
@Itolstoganov
Remove graph link check for diploid graphs
3a60d97
@Itolstoganov
Rename project
01a3518
@Itolstoganov
Add readme. Refactor command line
df73321
@Itolstoganov
Use metaFlye assembly info for meta mode
384f8b5
@Itolstoganov
Add relative score parameter
1e99614
@Itolstoganov
Add gaps or non-incident edges
35adf14
@Itolstoganov
Replace non-graph links with gaps regardless of origin
935f971
@Itolstoganov
Temporarily ignore simple vertices
f27983a
@Itolstoganov
Support tellseq libraries
43473bb
@Itolstoganov
Do not check first char in sequence
9154196
@Itolstoganov
Additional logging
2b280cc
@Itolstoganov
Downsampling option
347966d
@Itolstoganov
Fix downsampling
53e7e60
@Itolstoganov
Make downsampling actually uniform
0b893e4
@Itolstoganov
Add scaffold links. Recsue links from ambiguous vertices.
c6fc31e
@Itolstoganov
Use scaffold links in vertex resolution
8b6364b
@Itolstoganov
Fix index building from 10x format
4db98f1
@Itolstoganov
Refactor main. Remove unnecessary statistics. Fix\silence warnings.
58ab07f
@Itolstoganov
Remove path checker, refactor path extractor
9121636
@Itolstoganov
Remove long edge based statistics
1c4ac74
@Itolstoganov
Remove most of cloudspades
bd4a141
@Itolstoganov
Fix edge merging
df409cc
@Itolstoganov
Remove unnecessary logging. Postrebase fix
a8b11fb
@Itolstoganov
Ignore graph links for simple graphs
257b27d
@Itolstoganov
Update manual and cli
3c838cc
@Itolstoganov
Sparsify barcode edge coverage
fa5b336
@Itolstoganov
Postrebase fixes, restore main spades pipeline
90a6bf5
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@asl asl Awaiting requested review from asl

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3 participants
@Itolstoganov @asl @AntonBankevich