-e631ca3 (HEAD -> master, origin/master, origin/HEAD) unmask. update V
-7c5f69d masked hiv and measles tests
-c62ecba added pdf
-8bbc5e3 update paper
-fdb9ed0 update paper
-7a45469 update paper
-46d129d update paper
-8b00faf update paper
-7a2134f update paper
-47bce57 update paper
-0318e15 update paper
-20374c0 update paper
-968bb0f update paper
-3ee7c60 update paper
-0528d15 update paper
-2a4e844 joss draft renders
-e9078f6 joss draft renders
-c9b4b9c auto generate pdf
-b763518 auto generate pdf
-682010f auto generate pdf
-422986c auto generate pdf
-1e64873 readme, paper, updates
-b82acf6 readme, paper, updates
-d2ab92e readme, paper, updates
-1462ebd readme, paper, updates
-79565bc readme, paper, updates
-afd5413 (origin/readme) readme, paper, updates
-9b0896c updating the readme with tuts
-524ca55 update paper, tweak iqtree
-ac13ae4 24 core limit
-cee9b19 speed up iqtree2 stage
-916e5d1 removed resourceclass: large
-95a7fc1 build works nicely, resourceclass: large
-06d7792 run tests after build
-edd27f7 (origin/build) oldstyle yml works!
-c353a1d moved environment.yml back to old method
-eb96e6b moved environment.yml back to old method
-54bb36a updated install instructions
-de11241 updated version. build works!
-f239163 pinned all deps, moved pip installs to conda
-41e5f01 pinned all deps, moved pip installs to conda
-b5edcca pandas incompatible with py39! solved for pip then
-dd0e69d dumped pandas, as it breaks pip install
-2814d6c pinned and added py deps
-38f2f20 testing pip install
-5829176 removed git pull cmd
-0cb15eb unpinned pip
-e5594a4 switched to build branch
-dc4d3d8 added channels for py39andr403
-742e713 dumped mamba from workflow
-2f7565b added channel for mamba
-2008acf break
-157a121 unpinned R versions
-d019bca unpinned R versions
-0324951 (origin/builder) added conda update conda, new branch
-41b2dfd added conda update conda, new branch
-6c595f4 fixed config.yml
-0a66ea5 build works locally
-c82e7ea Removed R from channel list
-0ebebf4 Build, my pretties
-1ccf7b9 Build, my pretties
-bd39f40 ...
-f7835d7 not looking good at the moment
-7010c2f why
-f36b837 pinned py38 versions
-1a42858 :
-891bcc6 :
-e43a600 :
-3fd3e72 :::
-1955fcf :::
-f77df98 pressing the steam button
-4067460 pressing the steam button
-ab0f636 Ironing out the creases
-a86f786 Ironing the clothes
-14fdb98 fixed some edge cases. need to fix trimming for amplicon
-884c276 updated py38 to py39
-666978e Added validation data from PMC7259881
-9674e12 fixing install.sh
-839a87e testing
-6afeb11 Highlight tips
-b47cf5b tidy up
-99090ce Added HIV validation set from ClusterPicker repo
-d69a7a9 updates to readme
-faf229c papier mache
-6eef6c1 papier mache
-c381a5d mortein
-9f5394c moved depcheck to conda list
-cf6095a debug environment.yaml
-ffb1c84 debug environment.yaml
-11478be debug environment.yaml
-88ce70a debug environment.yaml
-1299fca debug environment.yaml
-64df429 environment.yaml replaces install.sh
-7d292ad bigger tests
-c9f2090 paper.md
-372a20d paper.md
-30c24da paper.md
-a1ed53e inflated the test suite
-efbfc9e wgs testing
-42ccad7 adding test data
-3cb54c4 adding test data
-6e6dc85 (origin/paper) Update docs, added wgs test, update paper.md
-e509fc3 paper.md
-808a97f paper.md
-37228eb paper.md
-2dfdd1f paper.md
-dc53ece update docs
-387dd1a update docs
-0da198a update docs
-4d8fa79 update docs
-473fcc7 update docs
-6f80b3d update docs
-501970f removed mouse hover
-40cf1f0 removed mouse hover
-56dc33c switched path to blob/master not docs
-27c4dc6 added figures
-2dad024 Updating docs
-d506b4d Updating docs
-4cad2cf Updating files table
-5d059a8 Updating files table
-e012bc4 Updating files table
-fd3f3d8 improvements to re-run and nomenclature
-d2e5157 Updated docs
-aba0d36 Updated setup.py
-4e71f03 Updated biopython, Bio.Alphabet is redundant. Debugged.
-fb10f8d adding yaml
-5243547 (origin/docs) docs
-9c1cffd add in images
-b70f5d9 add in images
-b496f57 add in images
-9a05861 add in images
-c8acf24 add in images
-9c21c70 updating documentation
-f485027 (origin/documentation) update documentation
-259db5b update docs
-599fec2 update docs
-bd4882f softcoded mapper
-28dd9c3 Update FAQs
-99f63d8 updating documentation
-0027e5a Test and works on SARS-CoV-2 WGS
-08587b2 havic works on SARS-CoV-2 (small scale test)
-0d2131c stop secondary and supplementary mapping
-ddb8662 tuning ggtree parameters
-dd833cd (origin/trimbug) Update package data list
-a04d23e Trims proper. Can use any genome now.
-2d69066 trying to debug trim
-1ff757f (origin/treeroot) Added tree-rooting option
-7348136 allow user to set root
-cc91e5e Runs now on test measles input, ref genome, and target region.
-a0d63b9 Runs now on test measles input, ref genome, and target region.
-972cc23 Update v no.
-8040159 Yes on force rerun
-495622d (origin/highlight_tip) SNP heatmap colors and annotations consistent with tree plots
-4fc3b8d Added tip highlight feature
-2bcf732 tip_highlighter feature
-eb32a16 tidy up the havic_detect.yaml
-1082b3a out of the dangerzone
-203a58a test on master. danger
-dae8c3f test on master. danger
-6b5c14b test on master. danger
-dc4bf95 test on master. danger
-74c77f8 test on master. danger
-d039665 test on master. danger
-c1e246a test on master. danger
-9f8f9fa Update version, package_data, stopped print of key, val.
-beb2696 Fixed bugs. Found a new one. Fixed it.
-ed217c3 fixing broken bits
-686d75b fixing broken bits
-8a1dceb moved R CMD BATCH to single line. BLACK broke it?
-49887bf debug install, fixed path
-ebf74e4 debug install
-e490a80 dangermouse
-dd507f6 dangermouse
-b0b5166 dangermouse
-b27482f dangermouse
-9773f6d dangermouse
-295faec ...
-3661615 Fixed dependency checks
-67b1444 pre-commit works, refactored depcheck
-cf9a292 pre-commit-config.yaml minced my program. Hours to fix
-ef40207 pre-commit hooks
-610b0f0 commenting out and cleaning
-8d10d1f cleaning master
-9b52c1f cleaning master
-592a7a9 cleanup
-3b2ba8b Updated .gitignore
-e95127f Updated circleCI link
-7b569c7 tidying up
-8fc517c (origin/tipnames) yaml works!
-74d0300 Fixed logic, building cmds
-5b06c8b Fixed logic, building cmds
-8cf67ab Fixed logic, building cmds
-477ba9d cleanup dir
-49ad166 pipeline re-run territory
-f62372e getting complicated
-1f9e66f updating refs to yaml
-63df4f5 dev on yaml config
-f25073a shifting over to yaml
-21337ec lowercased folder, updated version, commented out setup.py options
-6466fe9 implementing yaml
-0f5da0d Optimising settings via yaml
-8316fb6 Updated setup.py
-1b4fc8b Update version number
-452a074 (origin/fofn) Reads fofn in test suite
-fbb60c1 fofn dev
-97efebc fofn input refactoring
-19434d6 Reporting of duplicates and refactored headers
-691b28f (origin/pathlib) Refactored code to pathlib, removed redundancy
-50fd3ce Replaced os.path calls with Path calls
-eb438fa Refactoring to pathlib, removed Input_file class
-d6049da updated version number
-d5e3391 (origin/testsuite) Fully functional test suite
-13748ea functional test suite. todo: check output files
-351bc07 Refactored refamplicon import
-9b96672 rearranging havnet amplicon call and tests
-bab945a passing tests
-ee9849a about to merge testsuite into master
-61af022 Refseqer test passes
-807a912 first failing test
-90a5d69 First passing test
-03205b4 dev on testsuite
-13a50e8 Starting dev on testsuite
-973bff3 Update config.yml
-b859a5b fail it deliberately
-9bcbc3e Update README.md
-f9937b6 Update README.md
-d620d91 maybe its working
-3c05083 troubleshooting...
-d11df04 troubleshooting...
-67f4f65 troubleshooting...
-1f0c4e3 adding environment variables
-49a4de7 adding environment variable after activating env
-c6eccfc added which to list of installs
-4854ac8 .circleci debug, find clusterpicker
-06d5a8d .circleci debug, find clusterpicker
-79eccd7 .circleci debug, find clusterpicker
-4ac72d3 .circleci debug, find clusterpicker
-2969c55 .circleci debug, find clusterpicker
-7dc5ac2 .circleci debug, find clusterpicker
-827e3e8 .circleci debug, find clusterpicker
-8795fc6 .circleci debug, find clusterpicker
-ff2db6f .circleci debug, point to havic_env
-a145535 .circleci debug, comment out export PATH
-663d561 .circleci debug, comment out docker py38
-34a0470 .circleci debug, comment out docker py38
-30f9927 .circleci debug, activate env
-4c3bcee .circleci debug, forgot comma
-cdb5017 .circleci debug
-b0daf85 .circleci debug
-731cabb .circleci debug
-bdc7638 Fixing .circleci/config.yaml
-456a322 Fixing environment.yaml
-599c604 .circleci debug
-907b8af .circleci debug
-fe037fd .circleci debug
-a00a549 .circleci debug
-0a1c0c3 .circleci
-25fd99f conda environment.yaml and .circleci
-628ba06 Updated README.md
-fb13c90 (origin/trim_seqs) Fixed install instructions
-8acef64 Fixed trim_seqs bug, now fixing phytools install
-0518007 Updated install instructions, version
-4cb6bd2 Update README.md
-c9a7238 Updated install instructions for conda env
-2a9d77f (origin/dev) Fixed rpy2 error
-960924c Updating version number
-a9e4c4b removed plotly from install list
-f59ac95 removed library(plotly) from top of script
-33111b5 updated n proc
-2c2681a Added print to if statements
-8dbdfcd Added option to draw msaplot
-2cf69ba Removed -bnni option
-cef1da8 Added -bnni option to UFBootstrap test
-d080a20 No longer plots MSA
-b2220f8 Merge branch 'master' of https://github.com/schultzm/HAVIC
-cccff84 Removed ncolors
-99c6f8d Create cigar.py
-2af6326 rstrip \r from seq names
-3a04d97 replaces # in seq names with _
-bf13854 added test fasta seq with # in name
-f0e2920 Delete .ruffus_history.sqlite
-ab1344a Delete .RData
-47519d2 Update .gitignore
-7764edf updated version
-0b0dbed Added features to check (now depcheck)
-edc0828 changed name of check subparser to depcheck
-49823b9 Debugged trim alignment and ggtree align=T
-277826d Fixed /usr/bin/java bug
-57a74b2 Fixing Rout scripts and pdfs
-ddb27dc Fixed Rout files. Need to stop generation of Rout.pdf
-9fe81d3 Fixed n <3 alignment bug
-faa4239 Fixed custom ref seq pipeline path
-cc32322 Fixed temp SQLite DB bug
-a166ef6 Fixed temp SQLite DB bug
-1d57514 fixing outdir to tmp
-7594638 Moved SQLite db to tmp
-2cc4aaa added tidyverse
-2f36f92 Merge branch 'master' of https://github.com/schultzm/HAVIC added iqtree_threads
-b7d753c Added iqtree_threads option
-b5dcdb8 added matrixStats
-fd25949 added Biobase to deps
-d4a0031 added RCurl to dep list
-d760216 Fixed nexus to fasta in fastafrombam
-544c39d (origin/pipe_of_pipes) debug
-97f3f5b Creating a pipeline of pipelines
-5238146 Setting default None for args.trim_seqs
-aad0284 Added default to args.trim_seqs
-4c892ab debug
-d833633 debug
-9e3d068 Merge branch 'master' of https://github.com/schultzm/HAVIC
-8f389d6 debug
-d12c112 fixed edge case in clusterpicker path
-a01a98c Debugged FigTree bkp stage
-64047bf added backup function in pipeline
-3ccc776 added check to clusterpicker path exists before running
-fc7ec70 debugging clusterpicker function
-cc37daa allowing user specified path to clusterpicker
-e6caa1c removed rpy2 dependency. Moved to R CMD BATCH of *.R scripts
-5e9fcfb renamed pipeline steps
-9e4e4a2 renamed pipeline steps
-994c03a added outdir arg to get_execution_time function
-373e362 import os in runtime function
-a061e50 debug args.outdir print
-824809c fixed indent
-f4e649c Update main.py
-0d76a30 Update README.md
-9648659 fixed print of outdir
-1da862f added dev options for ruffus
-e6b9e6c moved ruffus at transform to at files
-ab3d524 fixing r plot
-4b70fd9 added test suite
-e6b15e1 adding test suite
-e10573d Refactoring
-378cfaa tidying up
-3eac9a4 re-implemented check_r_dependencies
-ac202a8 Update init.py
-55cae31 Update README.md
-afd0bac Update README.md
-9a910de Update README.md
-2fa6f02 Update README.md
-ba83afe Update README.md
-bbb4250 Update README.md
-2efbd8c Update README.md
-a26f52c Update README.md
-0e49556 Update README.md
-7c6c8b9 changed name
-1d990ab Update README.md
-3f6513d changing software name
-f8d019e (origin/ruffus) Ruffus pipeline working
-aceb42c fixed bug fontsize too small or ncluster == 0
-3e7b4bf fixed package data
-15321a7 added package data
-803c891 added pipeline_runner
-3d435f9 Merge branches 'master' and 'ruffus' of https://github.com/schultzm/HAVTrans into ruffus
-5303fb9 pipeline moved to class Pipeline
-7b7b53f moving run module external to main
-d595bfd cleaning
-510eb7c doctests to check_dependencies
-161a5b3 Git ignored .DS_Store files
-3d80022 Delete .DS_Store
-6d6bd0d Delete .DS_Store
-c3490ce Delete .DS_Store
-cd0fa54 (origin/internat_matches) Git ignored .DS_Store files
-7503c83 Git ignored .DS_Store files
-04a11e4 moved alignment trimming to Trimmed_alignment class
-eaaab63 gitignored .idea files from pycharm
-de5a2bb moved alignment trimming to Trimmed_alignment class
-4c5bc0e trimming refseq to remove 5' and 3' gap padding
-554a163 creating class to trim alignment
-6b161eb trimming db seqs in alignment based on refisolate
-9804c27 fixed imports of classes
-621127b moved classes to utils
-761315e Fixing plot parameters
-da16baa cleaning junk from code
-6dad71c IQTree back in pipeline
-f184e72 (origin/raxml) re-implemented iqtree
-d37030c raxml in pipe
-d1536a2 raxml cpu count
-a1bb050 finding ncpus for raxml
-aa25431 trying to calc cpus via patterns
-ac4eb34 iqtree working pipeline
-e8af492 Fixed labels bug. Tree manipulation ete3
-d44aa56 tidying up code
-092ed55 moved tree manipulation to ete3. biophylo fails quietly
-94942fc raxml trials
-ca92635 pylinting
-bf89669 pylinting
-04409a0 Merge branch 'master' of https://github.com/schultzm/HAVTrans
-cf6d1e9 Fixing plotting margins and colours
-c843d6a Fixing plotting margins and colours
-e48cb18 Fixing plotting margins and colours
-26d4f4c Fixing plotting margins and colours
-05ff969 Fixing plotting and titles
-64a5d3f Fixed snp_dist matrices
-d9ca104 Fixed snp_dist matrices
-3bd43f7 Fixed offset scaling, N snps fix
-9ac3e8f Added prefix function
-a420cc1 Fixed heatmap, added clust names
-fa48868 Fixing font size
-8e71d06 Fixing font size
-5ec0bac Fixed subject seq to prepackaged
-1f84a03 Added k-mer option
-8463f78 Fixed plotting and mapping
-ce57919 Prints nice pdfs
-558c48e updated version date
-051fa7a fixed plotting functions
-af4dc49 fixed plotting functions
-1cbd668 fixing r script
-40b0017 looper fixed
-c65101f looper fixed
-b23584b working on tree plot msa
-11753e4 adjusting ete3 parameters
-b5fd1b0 gitignore pychache
-5f6c992 Trims alignment, runs on trimmed
-7d694f3 Prints alignment next to tree, after trimming alignment
-9df467c Working pseudo-pipeline
-cf0347d Building package. Check dependencies
-fb63b65 Building package
-8a850bc Initial commit