Code

Upgrades to refinement functions#175

Code

Merged

nickjcroucher merged 187 commits intomasterbacpop/PopPUNK:masterfrom refine_fixbacpop/PopPUNK:refine_fixCopy head branch name to clipboardJul 29, 2021

+1,638-712

Commits

Commits on May 24, 2021

• Change individual boundary refinement

  nickjcroucher

  committed
  932075a

• Change GPU shared memory management

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  8acd320

• Import rmm package

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  5df8ee9

• Update refinement model assignment

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  e7767cd

Commits on May 25, 2021

• Fix network weights processing

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  committed
  2e2ea87

• Fix distmat subsetting

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  fb8dce9

• Fix list class check

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  d5ab4f0

• Load GPU packages for visualisation

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  746f236

• Load cugraph

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  609249c

• Convert cupy array to list

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  f03b3ee

• Fix function name

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  3feecf6

Commits on May 26, 2021

• Make sequence name processing consistent

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  5f54941

• Replace dots with underscores in names

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  300a851

• Replace dots with underscores in names correctly

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  7f7bb88

Commits on Jun 7, 2021

• Enable visualisation of individuall-refined clusters

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  91fe22a

• Simplify indiv-refine reading loop

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  7445d4c

• Save each refined graph to a different file

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  a0a0dad

• Enable querying with indiv-refine

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  e3d3b3c

Commits on Jun 8, 2021

• Enable querying of indiv-refine models

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  c15b6ba

• Enable output of separate networks with indiv-refine models

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  a05b92c

• Change processing of reference networks

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  a7406f3

• Fix reference expansion on query

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  d6477a3

• Sote indiv_refine status correctly

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  ac2b17a

Commits on Jun 9, 2021

• Change reference selection check

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  219c788

• Remove redundant dborder variable

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  82a9a31

• Use new network construction functions for assignment

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  d75842c

Commits on Jun 10, 2021

• Improve ref-query graph construction

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  4e921c6

• Fix ref-query edge additions

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  adfe2aa

• Fix query testing

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  af827ad

• Check for graph weights

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  2f07f0b

• Remove cupyx function

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  e0add4c

• Change GPU flag

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  9aedb5c

• Fix GPU network reference graph construction

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  e955ff0

Commits on Jun 11, 2021

• Edit messages when fetching network

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  91ff53c

• Fix selection of references with GPUs

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  a5757fd

• Alter GPU reference graph construction

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  cde0c91

• Update GPU graph loading

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  ce0ca1d

• Fix boolean argument

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  0f07027

• Update tests

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  d7b6752

• Change qq_dist update

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  1d5f12d

• Fix reference file writing

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  212dec5

• Enable deletion of random matches in HDF

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  71e1b01

• Fix edge weight calculation format

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  c8bfb6e

• Attempt to resolve GPU bus error

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  c0a27a9

• Remove attempt to resolve GPU bus error

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  8492787

Commits on Jun 13, 2021

• Change processing of previous networks with cugraph

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  4a57971

• Make edge tuples consistent

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  afdde8c

Commits on Jun 14, 2021

• Fix GPU tests

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  d220f22

• Fix GPU construction for single-edge graphs

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  cc2591f

Commits on Jun 15, 2021

• Change GPU package import

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  ed26be3

Commits on Jun 16, 2021

• Update pruning of sequences on model fitting

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  83f3438

Commits on Jul 2, 2021

• Merge with updated master branch

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  5647b24

• Avoid system recursion limit

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  2261e36

• Change legend position

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  69454e2

Commits on Jul 4, 2021

• Update GPU tests

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  1f0c78c

Commits on Jul 5, 2021

• Fix import of GPU libraries

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  0b26c31

• Update GPU command lines

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  7fec151

• Update reference pick to use GPU

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  41e7821

• Fix function load

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  53464cb

• Fix graph file name

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  e70b02a

Commits on Jul 6, 2021

• Save MST network

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  cf33f65

• Move MST network save

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  52d71e0

• Save Newick MST

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  70c14cc

• Change file mode

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  58ad996

Commits on Jul 7, 2021

• Overwrite not append for weighted networks

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  f25752d

• Remove quotations from dendropy newick strings

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  5ae2eab

• Remove quotations from dendropy newick strings

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  0e1f552

• Fix weighted network error

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  abecf50

• Change dense network construction

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  b88e05a

• Fix tuple generation

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  6fb579d

• Fix tuple generation

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  2379cde

• Fix tuple generation

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  6bb281e

• All dtype flexibility

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  149110f

• Change distance processing

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  0124b66

• Fix distmat name

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  0fcde0d

• Change network df construction

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  1c853e6

• Remove custom function as unnecessary

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  32b24d4

• Restore function for modification

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  dcf8afb

• Remove unneeded function after benchmarking

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  80c763f

• Remove function after further benchmarking

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  e8c978c

• Merge branch 'refine_fix' of https://github.com/johnlees/PopPUNK into refine_fix

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  edfe217

• Remove function after further benchmarking

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  4c500d1

• Merge branch 'refine_fix' of https://github.com/johnlees/PopPUNK into refine_fix

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  2f9c44d

• Update QC of query distances

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  d819829

• Merge branch 'refine_fix' of https://github.com/johnlees/PopPUNK into refine_fix

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  da348a9

• Update QC routines

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  3031454

• Merge branch 'refine_fix' of https://github.com/johnlees/PopPUNK into refine_fix

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  c7cc993

Commits on Jul 8, 2021

• Fix indexing of query values

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  8940556

• Make query functions consistent with arguments

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  a2dd161

• Merge branch 'refine_fix' of https://github.com/johnlees/PopPUNK into refine_fix

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  committed
  1ecaeff

• Remove jaccard wrapped from queries

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  121cdd3

• Merge branch 'refine_fix' of https://github.com/johnlees/PopPUNK into refine_fix

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  8985f5b

• Change string to list

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  c6b5cac

• Merge branch 'refine_fix' of https://github.com/johnlees/PopPUNK into refine_fix

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  99727bb

• Change to kmer list

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  e70812d

• Merge branch 'refine_fix' of https://github.com/johnlees/PopPUNK into refine_fix

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  committed
  ede9349

• Switch off GPUs for Jaccard calculation

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  46c1187

• Merge branch 'refine_fix' of https://github.com/johnlees/PopPUNK into refine_fix

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  committed
  326b183

• Change sketchlib function name

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  401271f

• Merge branch 'refine_fix' of https://github.com/johnlees/PopPUNK into refine_fix

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  committed
  057a6eb

• Fix fit example plotting for queries

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  committed
  30f9853

• Remove jaccardDist function

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  346c98c

• Use cupyx functions

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  committed
  678ac8a

• Update and document lineage assignment

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  08c7a02

Commits on Jul 12, 2021

• Visualisation using sparse distance matrix

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  0dc0745

• Update sparse MST arguments

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  b761599

• Fix visualisation rlist reading

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  1b1b525

• Fix use of previous data

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  dd81208

• Update command line arguments

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  b504f1f

• Fix function name in call

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  809d4ff

• Fix variable names

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  09daef0

• Remove check of undefined variable

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  a75b641

• Edit undefined variables

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  69ee541

• Change loading of previous MST

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  committed
  ab6e7fb

• Fix MST function call

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  dfb6639

• Change edges DF

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  7702ba5

• Merge branch 'refine_fix' of https://github.com/johnlees/PopPUNK into refine_fix

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  committed
  bb6012f

• Address possible bug in graph extraction

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  0ec7fb6

• Convert values to integers

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  adbcda4

• Fix variable name

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  ad531ab

• Process distmat for t-sne

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  committed
  83305e2

• Fix plotting for reference databases

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  fe8761a

• Fix plot fit isolate names

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  3241a0e

• Convert lists to arrays

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  ad8918d

Commits on Jul 13, 2021

• Generate networks from sparse matrices

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  f00f77d

• Ensure variable defined

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  c017d4c

• Test if rank_fit supplied

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  9f389d4

• Fix network construction from sparse matrices

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  be84f95

• Import function

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  f8dbdba

• Ensure variable always defined

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  badfba0

• Fix network output function

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  8cce9a8

• Only calculate MST once

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  eac9eea

• Add docstring for new function

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  9436228

• Add script for comparing network properties and sequence properties

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  105db6c

• Fix data frame properties

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  b5644cd

• Change sample ordering

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  52c4e35

• Change file name processing

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  2796773

• Enable sparse matrix processing

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  886e654

• Fix column ordering

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  adf7a62

• Fix column ordering

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  449f220

• Change column order on loading

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  3249f05

• Change column renaming

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  a9b84a9

• Change taxon ordering

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  a4ddb97

Commits on Jul 14, 2021

• Sort vertex order

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  6efdd84

• Remove unnecessary distance argument

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  e988561

Commits on Jul 15, 2021

• Define suffix variable

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  committed
  f4b2cd1

• Re-enable joining of databases with lineages

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  committed
  2fd9df2

Commits on Jul 27, 2021

• Remove unnecessary branch

  

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  2be55dd

• Check model type before assigning different modes

  

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  5054109

• Fix file name processing

  

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  3a5fb22

• Clarify conditional test

  

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  ec70882

• Fix section title

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  nickjcroucher

  and

  johnlees

  authored
  aeeb3dc

• Fix whitespace

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  nickjcroucher

  and

  johnlees

  authored
  d16b5da

• Require necessary function argument

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  nickjcroucher

  and

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  authored
  9e2ad62

• Fix whitespace

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  and

  johnlees

  authored
  722d9a1

• Fix section title

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  nickjcroucher

  and

  johnlees

  authored
  8098aab

• Tidy up function calls

  

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  7d1bd04

• Remove parentheses from isolate names

  

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  a8ffbd4

• Initialise weights list

  

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  2d70db8

• Clarify assert statement for references

  

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• Remove defaults

  

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  cc0f023

• Consolidate info scripts into new code

  

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  08276f5

• Update function docstring

  

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• Add info scripts

  

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• Fix compilation issues

  

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• Fix syntax error

  

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• Remove default values

  

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• Restructure functions

  

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• Bump version

  

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• Move default values

  

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• Fix model object reference

  

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• Update tuple generation function

  

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Commits on Jul 28, 2021

• Add missing brackets

  

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• Change args name

  

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  90be56d

• Change network loading

  

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  dc69a47

• Correct network file name processing

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  2a524eb

• Update tests for info and trees

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  26f2f04

• Fix info test commands

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  4af6078

• Change component analysis

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  cbfcdd6

• Update tuple generation functions

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  4d6c1a2

• Clarify model type variable names

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  0ec1bcc

• Correct tuple generation order

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  6f74e52

• Tidy up section headings

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  6a90918

• Update function arguments

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  e1a3ffd

Commits on Jul 29, 2021

• Fix graph suffix error

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  e81f6ff

• Correct network input file

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  8dffc61

• Check for strand-specific databases

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