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CHANGELOG.md

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Release Notes for Methylation Plugin

[Unreleased]

  • FIXED error with canvas methylation not displaying
  • UPDATED allc to bigwig script to handle gzip allc files

[v3.3.2] - 2018-07-10

  • ADDED dialog mode which opens dialog immediately after loading tracks
    • useful for screenshots
  • FIXED error where no methylation was shown
    • caused by change in JBrowse which didn't store BigWig source during feature creation
    • added source information after feature is created if not already specified

[v3.3.1] - 2017-09-15

  • ADDED 5hmC to extended modifications

[v3.3.0] - 2017-09-07

  • FIXED issue with animal configuration coloring when coloring was track specific
  • FIXED issue not showing fully methylated positions
  • UPDATED track menu to only include checkboxes for contexts present
  • ADDED "extended modifications" option which supports m4C and m6A
    • additional bigwig files
    • even when activated, CG/CHG/CHH are the default contexts
    • to include m4C and/or m6A, must be included in the "context" property of track configuration
    • nav bar has single button that opens a dialog to filter sequence contexts
  • UPDATED test data to include context combinations and animal coloring
  • UPDATED bigwig so users can use "CH" context when specifying context in trackList, and converts to "CHG" and "CHH"

[v3.2.0] - 2017-08-29

  • UPDATED stats for tracks
    • context specific bases covered, min, max, and mean
    • overall bases covered and mean

[v3.1.2] - 2017-08-22

  • FIXED bug with animal coloring

[v3.1.1] - 2017-08-17

  • minor bug fixes

[v3.1.0] - 2017-08-08

  • ADDED HTML style methylation tracks
    • each feature is now a html div element not painted to the canvas
    • this will be beneficial for screenshots since html div elements are editable in pdf/svg format

[v3.0.3] - 2017-08-02

  • minor bug fix with methylated option checkbox not being destroyed on chrm change

[v3.0.2] - 2017-07-13

  • FIXED error where the String method "includes" was not being supported by phantomJS

[v3.0.1] - 2017-06-20

  • Changed default of MethylPlot to only show methylated positions by default
  • Added print statement to plugin constructor

[v3.0.0] - 2017-06-19

  • Updated MethylPlot with a "ShowMethylatedOnly" option, when checked, it only shows "methylated" sites
    • Methylated sites are determined by the value in the bigwig file
    • Methylated sites have "1" in the 7th decimal position; unmethylated sites have "0"
    • This only works when bigwig files have been converted using allc_to_bigwig_pe_v3.py option
    • When this option is used for bigwig files converted with a different script, results will be incorrect.
  • For tracks converted with "allc_to_bigwig_pe_v3.py", use the "methylatedOption = true" in the configuration file.
  • Also updated to score mouseover score values are only shown for visible sites

[v2.3.1] - 2017-04-12

  • ADDED testing with jasmine

[v2.3.1] - 2016-10-03

  • FIXED issue with track checkbox id's

[v2.3.0] - 2016-08-26

  • ADDED animal-specific coloring

[v2.2.1] -2016-08-04

  • FIXED bug where specifying methylation contexts was ignored

[v2.2.0] - 2016-08-03

  • MethylBigWig uses lowest common zoom level between the contexts of the same track
    • previously, contexts could appear very different at certain zooms because they had different number of zoom levels

[v2.1.2] - 2016-07-22

  • showCG, showCHG, showCHH are part of default configs
  • this change is important for the screenshot plugin to work properly

[v2.1.1] - 2016-06-26

  • FIXED error with track checkboxes id when changing reference sequences

[v2.1.0] - 2016-06-26

  • Additional configuration option "context" that searches only for the specified contexts
    • necessary when not all (CG, CHG, CHH) are present
    • necessary when file extensions are not exactly '.bw.cg', '.bw.chg', '.bw.chh'
    • if not specified and file is missing, error is displayed on screen rather than ignoring the context

[v2.0.1] - 2016-06-24

  • REMOVED flag colors because they didn't work well with overlapping features

[v2.0.0‘ - 2016-06-24

  • Prefered methylation visualization track type "MethylPlot" which uses the "MethylBigWig" Store
    • MethylBigWig looks for three separate BigWig files based on context
    • Fixes the issues with context for zooming
  • Older methylation track is still supported as the MethylXYPlot using BigWig store.
  • New methylation track also uses color in mouseover value flags

[v1.2.2] - 2016-05-19

  • corrected track menu check boxes so it agrees with the toolbar enable/disable
  • track menu checkboxes have color that indicate methylation context

[v1.2.1] - 2016-02-15

  • UPDATED the methylation colors and buttons to be red-green color blind friendly
  • UPDATED allc_to_bigwig_pe.py script that renames chromosomes

[v1.2.0] - 2016-02-07

  • ADDED toolbar buttons to turn on/off methylation contexts for all tracks

[v1.1.0] - 2016-02-05

  • ADDED allC_to_bigwig.py script to be able to convert allC files
  • ADDED menu option to be able to change the height of all methylation tracks at once

[v1.0.0] - 2016-01-24

  • Initial release
  • Allows context-specific methylation data to be displayed in JBrowse