Code

v0.2.6#6

Code

Merged

ktmeaton merged 188 commits intomasterktmeaton/plague-phylogeography:masterfrom devktmeaton/plague-phylogeography:devCopy head branch name to clipboardApr 27, 2021

+53,181-1,492,518

Commits

Commits on Mar 3, 2021

• add 2020 Latvia samples to database

  ktmeaton

  committed
  2cd4a7e

• add 2020 Latvia samples to SRA

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  25421d9

• test results upload....

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  873d4a4

• test add qualimap results

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  e57f2a0

• remove qualimap results files, too many

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  d8265b4

• add results snippy_multi filter5 aln

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  988b47d

• create snakemake rule for parse_tree

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  03aac6b

• create snakemake rule for clock_model

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  4a53263

• try to clean results before running CI

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  c61a0ff

• create new script to backup results

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  ff68c7e

• remove comments in backup results script

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• remove plot_table rules and script

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  2ed3747

• test remove geo from version control

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  1275922

• add list mode to backup results

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  ff94ffb

• remove output files from version control

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  f0f1de4

• troubleshoot confidence errors

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  f35e391

• rerun pipeline ci when notebooks change

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  95d39c5

• add Denmark metadata to db

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  e4c16cb

• remove almost all attached files from report

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  1cdbcda

• add test dir to projects

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  645b185

• fix rule typos

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  78c7b94

• add test metadata

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  d368da9

• add dummy data for project main

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  22eb828

• rename main config file

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  9b9a589

• remove dummy main data

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  2ba19ee

Commits on Mar 4, 2021

• add rsync option to backup results

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  7fec05e

• change function identify_local_sample to use database

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  ddccc2f

• update metadata and config for denmark

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  9512900

• update metadata and config for project main

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  47c4c03

• create baitset project megapestis

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  1ecd956

• add baitsets to megapestis

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  cd84d90

• add project main iqtree

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  dd41821

• mark Latvia samples as low coverage

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  642e04b

• add project main local metadata

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  e74e5e9

• add project main multiqc

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  e0b9589

• Merge branch 'dev' of https://github.com/ktmeaton/plague-phylogeography into dev

  ktmeaton

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  d3d69d8

• Merge branch 'dev' of https://github.com/ktmeaton/plague-phylogeography into dev

  ktmeaton

  committed
  0ca751a

• add project main snippy multi

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  a3d51c5

• add project main detection

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  eece522

• add project main notebook output

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  ac19179

• redo the results backup clean restore scripts

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  ffcdab9

• parse_tree and clock_model work for test

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  3650614

• add clock plot to test project and report

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  2c98113

• update all target to include clock_plot

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  87cf425

• fix typo in results_restore

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  eec5a21

• remove duplicate record G701

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  99631a5

• add mugration_model and mugration_plot to snakemake

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  964a503

• add geo to snakemake

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  88edb8a

• add augur to environment

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  ff53f4e

• add parse tree df obj

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  f421e3e

• go back to ignoring obj files until testing

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  ab0355a

• add reference data to project main

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  154e130

• set load to 100 for jupyter notebooks

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  a03c9d2

• reset large file size again

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  d5ee647

• fix phylogeny indent typo

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  c984e13

• first attempt at plague-phylo full with jupyter snakemake

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  8f0ac25

• ignore megapestis project

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  0ec9046

Commits on Mar 5, 2021

• adapt locus coverage rule to analyze full genome

  ktmeaton

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  a5ba24b

• convert megapestis pPCP1 to fastq.gz

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  615e3e9

• add megapestis ppcp1 bam

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  e3c4c73

• add noncore to data and database

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  475f3cb

• add megapestis non-core bam

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  89cffd3

• finish megapestis project mapping

  ktmeaton

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  8ec324f

• Merge pull request #5 from ktmeaton/megapestis

  Show description for 7b5f05a
  ktmeaton

  authored
  7b5f05a

• mark which denmark samples have low coverage

  ktmeaton

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  53a4208

• new edits for locus coverage notebook

  ktmeaton

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  a19d280

• start plotting tree and heatmap as gridspec

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  747744a

Commits on Mar 6, 2021

• plot locus coverage for all genes on all plasmids

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  49b3755

Commits on Mar 8, 2021

• ignore locus_coverage_collect directory

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  1d306cb

Commits on Mar 10, 2021

• basic work on geo bias

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  f2f159f

• working on node connections for geo bias

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  9be9101

Commits on Mar 11, 2021

• learned how to use path effects

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  055ccc3

• arrow checkpoint before animation

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• first animation render

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  9b553fa

Commits on Mar 12, 2021

• checkpoint before redoing connections

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  bad7f30

• add animated map of branch 1.PRE

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  28d1f80

Commits on Mar 15, 2021

• create mp4 spreadmaps with ffmpeg

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  c6e5304

• animate branch 0.PRE

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  7109dc0

• animate branch 0.ANT4

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  d45722d

Commits on Mar 16, 2021

• add snp distance to environment

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  04167fc

• plot test snp_matrix

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  b1d03b4

• add snp matrix to snakemake

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  defe53c

Commits on Mar 17, 2021

• checkpoint before redoing plot aspect

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  7f63c19

• update dev notes

  ktmeaton

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  29c74f4

• switch targets to input

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  5ff707e

• uninstall and remove lfs

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  58a0c2c

• remove flowdash bio from profiles and update snp matrix

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  0d1c089

• remove results folder from docs

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  1604a2c

• remove docs-old and outdated report rst

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  0a70215

• update detect snp density collect rule

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  6561bd4

• cleanup in prep for project migration

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  644690e

Commits on Mar 23, 2021

• backup main project

  ktmeaton

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  38fbd76

• specific configfile param for workflows

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  4fdb363

Commits on Mar 24, 2021

• update script permissions

  ktmeaton

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  225bd2b

• set simple strict clock as model for testing

  ktmeaton

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  77d612a

Commits on Mar 29, 2021

• remove skyline plot from tracked snakemake output

  ktmeaton

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  5dbe20c

• update filter targets

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• update extract targets

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  f7b0522

• renable publishing remote auspice

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  bdb6f4f

Commits on Mar 30, 2021

• test remote json for modern parse-tree

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  e60fcd7

• rename remote json

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  1aff367

• add beast and beagle to conda

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  b79c7fc

Commits on Mar 31, 2021

• downgrade beast to 2.6.2

  ktmeaton

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  790b92b

• update project scripts

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  ced73b8

Commits on Apr 2, 2021

• change rate variation branch to rate rather than multiplier

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  ecfa6ad

• dont unload config file

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  55c6fb1

• clean config dir in script

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  f9952c4

• update clock scripts with better plotting and catch

  ktmeaton

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  95fd14e

• reset project clean config to correct original

  ktmeaton

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  4b0ea23

• new plotting for marginal date ranges

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  954e636

Commits on Apr 4, 2021

• add plotting root marginal distribution to clock plot

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  407c39e

• generalize the node dating plot

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  fd0b092

• working on comparing branches

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  00cb989

Commits on Apr 5, 2021

• make separate plots for tip date comparison

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  6fcaf35

• finish up clock plot distributions

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  207a892

• remove jupyter targets from all

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  af6c22f

• save inprogress work optimizing clock

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  8bb76cb

Commits on Apr 7, 2021

• add javascript code for an arcdiagram

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  5ff89fe

• rename arc diagram html

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  c13fe42

• add continent to metadata

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  ea703cb

• more coloring options for arc diagram

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  6022273

• fix path coloring for arc diagram

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  db61673

• make diagram slightly narrower

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  614327a

Commits on Apr 8, 2021

• update notebooks and env

  ktmeaton

  committed
  ae2e701

• Merge branch 'dev' of https://github.com/ktmeaton/plague-phylogeography into dev

  ktmeaton

  committed
  337baaf

Commits on Apr 12, 2021

• test projects for geo

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  2939280

• continue troubleshooting run and beast

  ktmeaton

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  4b1075a

Commits on Apr 13, 2021

• remove 2med lab strain

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  9a042e6

• remove duplicate record A1122

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  06b960d

• update filter sites and plot missing data scripts

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  477462d

• fix jupyter errors in plot missing data

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  24772de

Commits on Apr 14, 2021

• remove russian samples with no province

  ktmeaton

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  71fa9c3

• start changing column names to lower

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  ef5b713

• remove checkpoint file

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  5e06176

• convert column names to lowercase clocl

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  9c4f242

Commits on Apr 15, 2021

• overhaul directory structure and re-enable jupyter notebooks

  ktmeaton

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  a87ee70

• fix clock_plot target typo

  ktmeaton

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  c7566fc

• add placement comments to db

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  4713040

• try better path for trace log

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  187b5ce

• upgrade iqtree

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  602f067

Commits on Apr 16, 2021

• test iqtree lsd dating

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  d3e2625

• add beast conversion info for lsd

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  4312e9c

• remove old project folder

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  235a8f6

• update placement comments in db

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  01439e7

• remove notebooks as target

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  992e07f

• add alignment pruning to workflow

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  4ab7d14

• prune using branch lengths

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  0dba65c

• stable run for lsd placement

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  1977f37

• update beast prep rule

  ktmeaton

  committed
  7a9ebd1

• fix targets and scripts typo

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  committed
  2a4df5d

• set model in lsd

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  63d428c

• add execut permissions to script

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  d5543d7

Commits on Apr 17, 2021

• add outgroup to database

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  4f02172

• tree manipulation and filtering for beast

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  70089e2

• remove iqtree_scf rule

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  177b89b

• filtering alignments for beast

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  ef50cc9

Commits on Apr 18, 2021

• add outgroup metadata and catch in pruning

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  affe3a5

• remove constant sites in script prune_alignment

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  89280ac

• implement filtering for each step in phylo

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  ad41e99

• add some fixes to targets

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  058a5cc

Commits on Apr 19, 2021

• downgrade beast2 to beast1

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  f8e76ad

• revert default config to test

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  28af620

Commits on Apr 20, 2021

• update pruning and filter to write log

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  6a5f500

• nice rtt plots for prune

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  cd1b885

Commits on Apr 21, 2021

• possible fix for branch length precision

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  7361ecd

• print eager output to stdout for troubleshooting

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  cab6959

• switch to lsd2 from source

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  64c53ba

• remove outgroups in lsd stage

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  0cde5c1

Commits on Apr 22, 2021

• add map plotting to notebook

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  7c67702

• add timeline to plotting

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  e3b0afc

Commits on Apr 23, 2021

• mega plotting update

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  35ce044

• extra params for lsd2

  ktmeaton

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  4623efb

• first round of plot phylo with compatability for spread3

  ktmeaton

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  bb0f9ce

Commits on Apr 24, 2021

• renable eager log

  ktmeaton

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  035c929

• catch constant sites in filter script

  ktmeaton

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  cd6f133

Commits on Apr 26, 2021

• extract and plot subtree

  ktmeaton

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  cd24348

• Merge branch 'dev' of https://github.com/ktmeaton/plague-phylogeography into dev

  ktmeaton

  committed
  cfbc469

• restore eager log and fix typo

  ktmeaton

  committed
  3acb65f

Commits on Apr 27, 2021

• first attempt at fixing eager CI

  ktmeaton

  committed
  3790bdd

• remove eager log from output and command

  ktmeaton

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  62c1c5c

• fix typo in eager_tsv script

  ktmeaton

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  f36ae76

• add new rule to filter outgroup from iqtree

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  2169f03

• fix typo in metadata script

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  5dd79f8

• fix bug in filter_sites

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  2d5b754

• add more date col to metadata

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  8fba8a6

• fix branch lengths in conversion scripts

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  c309726

• create newick and nexus trees for beast

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  b24b1d9

• update docs notes

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  4e43f4f