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CHANGELOG.md

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CHANGELOG

NPM_0.1.27 - NPM_0.1.29

  • Added an extra check at the .github/workflows/sync-public.yml to check if public exists to prevent the workflow from erring. To use the workflow replace 'your-user-name/your-repo' with the correct values from your fork. This should synchronize your public branch with I-PV's master once a day.

NPM_0.1.24 - NPM_0.1.26

  • Added sync-public.yml which is a azure.yaml equivalent of syncing public branch of your fork. Keep this workflow in your master if you want the scheduled cron jobs to take effect
  • Converted http:// resources to protocol relative URIs in i-pv/circos-p/templates/javascript.txt

NPM_0.1.19 - NPM_0.1.23 / IPV_2.5

  • Below fields are now optional:
    • variation.fileName
    • variation.skipHeader
    • variation.separator
    • variation.colSubsType
    • variation.colValStat
    • variation.colGeneStrand
    • variation.transcriptID
    • variation.colPolyphen2
    • variation.colSift2
    • variation.maf
  • Added circos.cleanup parameter that only leaves the *.html as output and removes rest of the complementary files.
  • Added circos.perms that sets the permissions on the output files
  • Added datatracks.perms that sets the permissions on the output files.

NPM_0.1.12 - NPM_0.1.18

  • Added $(BRANCH_NAME) variable to azure.yaml
  • Modified docker/js/getFiles.js to include node directory entry objects (dirent) that either pass dirent.isFile() or dirent.isSymbolicLink() to correctly list available binaries.

NPM_0.1.8 - NPM_0.1.11

  • Various bug fixes
  • Added $(BRANCH_NAME) variable to azure.yaml
  • Binaries are logged on when docker is started

NPM_0.1.6 - NPM_0.1.7

  • Changed syncMirror to update tags.

NPM_0.1.5

  • Changed syncMirror to ignore stderr when process exits with 0. (See)

NPM_0.1.4 / IPV_2.4

  • Updated mirroring function syncMirror.
  • Added azure.yaml.

NPM_0.1.3 / IPV_2.3

  • Updates to readme and documentation of config options.
  • Minor bug fixes.

NPM_0.1.2 / IPV_2.2

  • Update .gitattributes to prevent auto EOL conversion for files under templates/

NPM_0.1.1 / IPV_2.1

  • Automatically transliterates backslashes to forward slashes in the config.json.
  • Prohibits use of \ / . ? * ¥ characters in name field of config.json and generated file names.
  • EOL conversion to Unix for files under templates/
  • Bug fixes for Linux cross-compatibility

NPM_0.1.0 / IPV_2.0

  • Added a JSON configuration option --config xyz.json that allows the user to generate images, bypassing manual provision of arguments. Especially usefull if you want to generate multiple figures on the fly and do not want to manually type in yes/no questions through STDIN
  • No need to modify my $circos path inside SNPtoAA.pl, automatically uses the circos.pm inside the repo folder.
  • Removed 2 copies of circos folder, now the there is only a single folder and it does not trigger the unescaped left brace warning.
  • Bug fixes

NPM_0.0.3 / IPV_1.47

  • Updated version string in SNPtoAA.pl
  • Version number is removed from package.json's main entry point. Regarless of versions, entry point will be same (SNPtoAA.pl).
  • Removed extra copies of ACE2 and Sars-Cov-2 spike examples
  • Added FindBin module from relativePathPropositon branch to remedy potential issues with relative paths in different OSs