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Merge SpLitteR#1366

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Itolstoganov wants to merge 158 commits intomainablab/spades:mainfrom hifi-tellseqablab/spades:hifi-tellseqCopy head branch name to clipboard

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Commits

Commits on Apr 30, 2024

• Some small include cleanup

  asl

  committed
  d5ce5d4

Commits on Jul 22, 2024

• Add example gfa splitter

  

  asl

  authored and

  Itolstoganov

  committed
  a83a25f

• Split GFA paths as well

  

  asl

  authored and

  Itolstoganov

  committed
  005ebb7

• Switch to new GFA parser

  

  asl

  authored and

  Itolstoganov

  committed
  533ac5e

• Add link info to vertices. Fix graph reading

  Itolstoganov

  committed
  055bd0c

• Split GFA paths as well

  

  asl

  authored and

  Itolstoganov

  committed
  5bdf83c

• Initial commit

  Show description for 53bb961
  Itolstoganov

  committed
  53bb961

• Added serialization

  Itolstoganov

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  73cd059

• Changed main data structure to pair of separate maps for head and tail of the edge

  Itolstoganov

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  ee3a22e

• Added visualization

  

  itolstoganov

  authored and

  Itolstoganov

  committed
  a88e3b7

• Changed barcode mapper structure

  Itolstoganov

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  b3aacb3

• Changed BarcodeMapper structure

  Itolstoganov

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  f65b655

• Find following edges via dijkstra

  

  itolstoganov

  authored and

  Itolstoganov

  committed
  3454721

• Changed barcode score. Added path scaffolder. Paired-end stages

  

  itolstoganov

  authored and

  Itolstoganov

  committed
  ad66757

• Added relative threshold to extension chooser

  

  itolstoganov

  authored and

  Itolstoganov

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  6d5829a

• Io refactoring

  Itolstoganov

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  3b3aee8

• Changed coverage checks in PathJoiner

  Itolstoganov

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  96c2d69

• Changed high coverage threshold (meaningless commit)

  Itolstoganov

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  e5ed92c

• Made changes according to the newest version

  Itolstoganov

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  0a4669e

• Added threshold on relative barcode coverage

  Itolstoganov

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  2b8815b

• Barcode threshold now depends on gap length

  Itolstoganov

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  e40248c

• Basic 10X support. BarcodeMapper refactoring

  Itolstoganov

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  5893ae0

• Added 10X statistics

  Itolstoganov

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  0ca8890

• Merged rr into general pipeline

  Itolstoganov

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  28d117f

• Added backward check in read cloud resolver

  Itolstoganov

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  3cffa98

• Separated storage from info extraction in BarcodeIndex. Various filters

  Itolstoganov

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  b5bc3c1

• added new type of library: Clouds10x and new spades.py parameter --gemcode1-1, --gemcode1-2

  

  AntonBankevich

  authored and

  Itolstoganov

  committed
  512d4f8

• Documentation stub. Added method that allows to get reliable barcode intersection of two edges. Clouds10x libraries now have the same rights as PairedEnd

  Itolstoganov

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  37b211e

• Moved statistics into separate project

  Itolstoganov

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  13ed588

• Removed gap closer optimization cutoff. Fixed online_vis. Added separate unique storage for read cloud resolver

  Itolstoganov

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  492de69

• Fixed initial filter validation

  Itolstoganov

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  25d5e94

• Added closest edge topology check

  Itolstoganov

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  7d7985f

• Added dijkstra based on paired info scaffolding

  Itolstoganov

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  846ffce

• Added command that prints barcode info to online_vis. Added more reliable barcode statistics

  Itolstoganov

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  b456c73

• Added parametrized gap distribution to read cloud statistics

  Itolstoganov

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  29eb8e8

• first version of read cloud based polisher

  Itolstoganov

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  87a0a5d

• Added paired-end polisher. Removed dijkstra polisher

  Itolstoganov

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  1c1f6e0

• Check for coverage breaks in the absence of candidates

  Itolstoganov

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  f5cf461

• Add transition statistics

  Itolstoganov

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  886a20e

• Enable cloud gap closer. Add capacity stats.

  Itolstoganov

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  d3a0630

• Lengthen the regions of the long edges from which barcodes are extracted

  Itolstoganov

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  e90591b

• Add read cloud clusters extraction. Extract barcodes from the end of the path instead of single edge.

  Itolstoganov

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  695cb76

• Change configs. Extract barcodes from the beginning of the candidate in the initial read cloud filter. Add barcode path connection statistics.

  Itolstoganov

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  33b92c4

• Add reference path connection statistics. Filter transitions from non-path clusters.

  Itolstoganov

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  2935900

• Store total number of barcodes in barcode index

  Itolstoganov

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  0a255ce

• Add scaffold graph construction pipeline. Add new statistics stages.

  Itolstoganov

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  2a2c992

• Implement composite connection predicate

  Itolstoganov

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  2278f52

• Add scaffolding resolver to spades pipeline

  Itolstoganov

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  0b915a7

• Add ScaffoldVertex interface. Generalize scaffold graph constructing algorithms. Add ScaffoldVertex index hierarchy.

  Itolstoganov

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  e22d390

• Add read cloud path scaffolder

  Itolstoganov

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  708efd3

• Use new scoring functions in read cloud path polisher.

  Itolstoganov

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  f8f0e10

• Add reference validation mode.

  Itolstoganov

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  63dcfae

• Save scaffold graph after initial construction

  Itolstoganov

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  319d67b

• Use containment index as main score. Add more statistics to validation.

  Itolstoganov

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  f9b54db

• Introduce new barcode connection criteria

  Itolstoganov

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  8a6e22a

• Automatic detection of containment index threshold

  Itolstoganov

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  ae7dc9b

• Improve read cloud path polishing

  Itolstoganov

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  d05f76b

• Cluster storage can be created from path scaffold graph

  Itolstoganov

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  f1870f4

• Add barcode connection scaffolding

  Itolstoganov

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  bf9386a

• Add recording barcode connection predicate. Add print long edge command. Refactor scaffold graph constructon pipeline

  Itolstoganov

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  1b1007b

• Add read cloud scaffold graph gap closer

  Itolstoganov

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  485fb64

• Use barcodes from unique edges only in EntryCollector. Change score in read cloud extension chooser.

  Itolstoganov

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  489a5cb

• Add basic scaffolding procedure to scaffold graph gap close

  Itolstoganov

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  2587b8c

• Add partial construction callers documentation

  Itolstoganov

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  5d86d76

• Add read cloud path extender to path extend pipeline

  Itolstoganov

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  c27f308

• Analyze paired-end scaffolder results

  Itolstoganov

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  26c304b

• Add score threshold estimation based on segments of long edges. Add short edge score estimator.

  Itolstoganov

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  c34cfe3

• Integrate short edge score and score estimator into scaffold graph construction pipeline.

  Itolstoganov

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  4cba21a

• Estimate training assembly graph edge length.

  Itolstoganov

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  51d8606

• Estimate training edge length for cluster statistics extraction. Incorprorate simple barcode filter into the search of initial candatates for read cloud extender

  Itolstoganov

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  e296461

• Add top min filter for read cloud extender. Serialize cloud distributions. Set resolvable repeat length as cluster length percentile.

  Itolstoganov

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  8512ed6

• Add 10x info in manual and help. Add path cluster statistics

  Itolstoganov

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  39407ad

• Add path extraction procedure to scaffold graph polisher

  Itolstoganov

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  50fff85

• Change scaffold graph polisher behaviour: remove repeat vertices, use cloud path extractor

  Itolstoganov

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  20b2ff3

• Add new long-edge cloud extraction procedure

  Itolstoganov

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  33523ee

• Add cloud filtering procedure

  Itolstoganov

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  c7fa066

• Contracted graph simplification. Support path vertices in scaffold graph validation procedure.

  Itolstoganov

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  f8e59a8

• Change transitive filter threshold

  Itolstoganov

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  411cfd6

• Simple barcode index binary serialization

  Itolstoganov

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  2285111

• Remove scaffold graph-related stages. Remove old statistics project

  Itolstoganov

  committed
  f759cfc

• Reorganize paths and namespaces, remove scaffold graph storage

  Itolstoganov

  committed
  ffa4e59

• Turn off path scaffolding in preliminary rr

  Itolstoganov

  committed
  3d01271

• ьReformat read cloud contigs, remove unnecessary boost file. Extender searcher fix. Optimize barcode index saves. Move read cloud configs to path extend

  Itolstoganov

  committed
  1b98132

• Refactor scaffold graph construction pipeline

  

  itolstoganov cn

  authored and

  Itolstoganov

  committed
  802fae0

• Scaffold graph validation improvements

  

  itolstoganov cn

  authored and

  Itolstoganov

  committed
  5fbf4df

• Postrebase fixes. Turn off searching extender and path extender path polisher for now. Dirty fix for transition extractor

  Itolstoganov

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  387c94a

• Initial containment index extractor

  Itolstoganov

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  46eff64

• Path storage extractor

  Itolstoganov

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  cb630c1

• Add hifi scaffold graph construction, path cluster extractor fix

  Itolstoganov

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  03185d8

• Barcode index construction optimization

  Itolstoganov

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  42bdae3

• Update barcode index

  Itolstoganov

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  3820336

• Construct scaffold graph using reversed index

  Itolstoganov

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  5741a44

• Use ReadProcessor for barcode index construction. Part 1

  Itolstoganov

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  db8a57e

• Use ReadProcessor for barcode index construction. Part 2

  Itolstoganov

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  effd185

• Conjugate edges and reads fix

  Itolstoganov

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  98a2217

• Add scaffold graph serialization, minor refactoring

  Itolstoganov

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  280cfa6

• Add iterator-based scaffold graph constructor

  Itolstoganov

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  818f1e7

• Iterator graph constructor optimization

  Itolstoganov

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  1458176

• Long edge cluster stats. Scaffold graph comparison

  Itolstoganov

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  ef19ec9

• Add HiFi links parser. Compare HiFi and TellSeq scores.

  Itolstoganov

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  2bbbad7

• Ensure we can create edge index with non-default k-mers. Only unique k-mers do count

  

  asl

  authored and

  Itolstoganov

  committed
  b173afe

• Add short kmer sequence mapper

  

  asl

  authored and

  Itolstoganov

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  affea42

• Iterator based intersection

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  fb12dab

• Jaccard index output

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  2eee080

• Add reference validation

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  306e148

• Add multiplex dbg reading

  Itolstoganov

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  c68db4a

• Cut edges during multiplex graph reading

  Itolstoganov

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  adbf6e9

• Change multiplex graph only in multi-edge neighbourhood

  Itolstoganov

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  2ab1ef6

• Add double coverage stat, refactor reference path checker

  Itolstoganov

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  4afdf05

• Add 3-path extraction

  Itolstoganov

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  f96078c

• Add two kmer mapper and vertex statistics

  Itolstoganov

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  4a0257b

• Uncomressed vertex statistics

  Itolstoganov

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  86b4661

• Use simple blunt graphs

  Itolstoganov

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  1610e8c

• Print covered vertices

  Itolstoganov

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  6e7cf36

• Vertex resolver refactoring, pt 1

  Itolstoganov

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  8d3ec85

• Vertex resolver refactoring, pt 2

  Itolstoganov

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  a8a077a

• Simple path extraction

  Itolstoganov

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  c4ca48b

• Process multiple libs

  Itolstoganov

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  8c8e143

• Increase default tail threshold

  Itolstoganov

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  29773f7

• Postrebase fixes

  Itolstoganov

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  652a466

• Add path support

  Itolstoganov

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  622d29d

• Path statistics, add single edges

  Itolstoganov

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  ad7e8b0

• Small path fixes, graph output

  Itolstoganov

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  dbe4343

• Fix merging

  Itolstoganov

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  8d62f5a

• Fix edge merging overlap bug, some refactoring

  Itolstoganov

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  18f9a84

• Support complex links for split

  Itolstoganov

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  95e32c7

• Support edge merging

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  2d3bbc5

• Add meta mode. Use contracted graph for VertexResolver

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  cad1182

• Fix contig output for contracted graphs

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  f47392c

• Check if linked-read links are supported by the graph

  Itolstoganov

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  c32d1cc

• Split partially resolved vertices

  Itolstoganov

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  201dfb9

• Remove graph link check for diploid graphs

  

  Ivan Tolstoganov

  authored and

  Itolstoganov

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  3a60d97

• Rename project

  Itolstoganov

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  01a3518

• Add readme. Refactor command line

  Itolstoganov

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  df73321

• Use metaFlye assembly info for meta mode

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  384f8b5

• Add relative score parameter

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  1e99614

• Add gaps or non-incident edges

  Itolstoganov

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  35adf14

• Replace non-graph links with gaps regardless of origin

  Itolstoganov

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  935f971

• Temporarily ignore simple vertices

  

  Ivan Tolstoganov

  authored and

  Itolstoganov

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  f27983a

• Support tellseq libraries

  Itolstoganov

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  43473bb

• Do not check first char in sequence

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  9154196

• Additional logging

  Itolstoganov

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  2b280cc

• Downsampling option

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  347966d

• Fix downsampling

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  53e7e60

• Make downsampling actually uniform

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  0b893e4

• Add scaffold links. Recsue links from ambiguous vertices.

  Itolstoganov

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  c6fc31e

• Use scaffold links in vertex resolution

  Itolstoganov

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  8b6364b

• Fix index building from 10x format

  Itolstoganov

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  4db98f1

• Refactor main. Remove unnecessary statistics. Fix\silence warnings.

  Itolstoganov

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  58ab07f

• Remove path checker, refactor path extractor

  Itolstoganov

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  9121636

• Remove long edge based statistics

  Itolstoganov

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  1c4ac74

• Remove most of cloudspades

  Itolstoganov

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  bd4a141

• Fix edge merging

  Itolstoganov

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  df409cc

• Remove unnecessary logging. Postrebase fix

  Itolstoganov

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  a8b11fb

• Ignore graph links for simple graphs

  Itolstoganov

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  257b27d

• Update manual and cli

  Itolstoganov

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  3c838cc

• Sparsify barcode edge coverage

  Itolstoganov

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  fa5b336

Commits on Jul 30, 2024

• Postrebase fixes, restore main spades pipeline

  Itolstoganov

  committed
  90a6bf5