Release notes

v1.11.8

• Remove react-bootstrap from the GenomePositionSearchBox
• Make vertical chromosome labels as well as loading status labels readable in vertical tracks
• Added an option menu item for rectangle domain fill opacity
• Added a parameter in zoomToGene to allow specifying padding around gene
• Add data fetchers to AVAILABLE_FOR_PLUGINS
• Update track list in AVAILABLE_FOR_PLUGINS
• Correctly setup initial scales of vertical tracks when the width of a center track is zero.
• Config-wise, allow axis-specific location locks (e.g., lock the vertical axis in a view to the horizontal axis in another).
• Add reload implementation to HiGlassComponenet API.

Detailed changes since v1.11.5

v1.11.7

• Show visual clue when tileset info is not available ("Tileset info not found. ...").
• Properly initialize the style of 1D brushes (viewport-projection-horizontal and viewport-projection-vertical).

Detailed changes since v1.11.5

v1.11.6

• Allow implementing plugin viewport projection tracks using config.projection.
• Change the default value of zoomLimits to [1, null], which means highest zoom resolution is 1bp.

Detailed changes since v1.11.5

v1.11.5

• Add a zoomToGene API that allows to zoom a HiGlass view to a location near a certain gene.
• Add a suggestGene API that returns a list of genes of top match for a given keyword based on autocompleteServer.
• Add a top-level option, compactLayout, that controls to allow adding vertical gaps between views.

Detailed changes since v1.11.4

v1.11.4

• Fix colorbar error on degenerate colorscale
• Update horizontal heatmap to regular heatmap rendering so that they can use the same options

Detailed changes since v1.11.3

v1.11.3

• Show a more comprehensive list of track types in the track config menu
• Break up HiGlassComponentTests
• Show only integer ticks in HorizontalChromosomeLabels tracks because it is misleading to have decimal values in genomic coordinates.
• Add a reverseOrientation option in HorizontalChromosomeLabels tracks to allow aligning tick labels and lines on the top or left.
• Make overlays SVG exportable
• Fix a bug that led to the app crash when selectRows is set to an empty array []
• Break up and turn off some tests
• Fix gene annotation mouseover

Detailed changes since v1.11.2

v1.11.2

• Fix registration of plugin tracks
• Don't try to render names of filler annotations

Detailed changes since v1.11.1

v1.11.1

• Fix multivec SVG export
• Added ChromosomeInfo and SearchField classes to AVAILABLE_TO_PLUGINS.

Detailed changes since v1.11.0

v1.11.0

• Make gene annotations rotatable so that they can be added on the left
• Tracks can now modify their own dimensions by publishing trackDimensionsModified.
• Fixed a bug preventing usage of data.url and HorizontalMultivecTrack server-side aggregation simultaneously.
• Fixed a bug preventing an updated value of track.options.selectRows from triggering a HorizontalMultivecTrack track update when using server-side aggregation (track.options.selectRowsAggregationMethod === 'server').
• Added the JS API .on('geneSearch', callback) option for subscribing to gene search events.
• Simplify plugin track registry
• Implemented plugin data fetchers.

Detailed changes since v1.10.2

v1.10.2

• Remove view config validation from hgApi.getViewConfig() and hgApi.setViewConfig() and instead move it into a new method called hgApi.validateViewConfig(viewConfig, { verbose: false } = {})

Detailed changes since v1.10.1

v1.10.1

• Remove text/plain encoding from tile proxy text fetcher
• Added the selectRowsAggregationMethod option for the horizontal-multivec track to enable server-side aggregation if set to "server" rather than the default "client".
• In the view config, moved the fileUrl track property under the data property: data: { url, server, filetype }.

Detailed changes since v1.10.0

v1.10.0

• Fixed horizontal and vertical cross sections
• Changed the style for the mouse over dialog to have a maximum width of 50 and to break words so that it doesn't go off the screen if there's a very long mouseover text.
• Lower the default annotation height in the Gene Annotations track
• Colors for rules
• Ability to load genome position search box chromosome sizes from an arbitrary location
• Plugin tracks can provide their own config menu options
• Remove horizontal-_ and vertical-_ prefixes from track names
• Load matrices with "None" data transform without crashing
• Add a view for showing schema log messages when JSON codes are edited in a config view.

Detailed changes since v1.9.5

v1.9.5

• Removed styles for naked td tag
• Reader for text genbank data (i.e. not pulled from a url)

Detailed changes since v1.9.4

v1.9.4

• Added the resolveImmediately parameter to the setViewConfig API call.
• Zooming can now be restricted by specifying zoomLimits in the viewconf.
• Fixed bug where the track config menu improperly positioned when clicked twice.
• Update the heatmap option interface to allow seeing the preview when a color picker is opened.
• Display an error message on tiles with errors in them
• Don't try to assign a color value scale if the colorEncoding is set to itemRgb. itemRgb means that the color is present directly in the annotation
• Add an option to separate the + / - strand annotations in the bedlike track

Detailed changes since v1.9.3

v1.9.3

• Consolidated track options of horizontal and vertical tracks
• Set background of new heatmap tracks in a combined track to transparent when added via the track context menu.
• Fixed bug where heatmap labels could not be hidden.
• The position of labels and colorbars for split heatmaps can now be changed.
• Use itemRgb field in bed files as the default coloring for bedlike tracks

Detailed changes since v1.9.2

v1.9.2

• Fixed divided tracks bug by adding denseDataExtrema
• Fixed divergent bar track
• Made the bar track compatible with the local tile fetcher
• Added fontColor, fontSize and fillOpacity options to BedLikeTrack
• Added cheat code for making the component editable (i.e. with headers)
• Fixed track names in config menu
• Keep locks on track type change
• Fix crashing higlass on non-existent value scale lock member

Detailed changes since v1.9.1

v1.9.1

• Used stretchRects to ensure that there are no rendering artifacts when zooming in too far
• Added scaled as a potential value to the annotationHeight option
• Added the maxAnnotationHeight option to limit the size of annotations when using the scaled option for annotationHeight
• Added the fontSize option for bedlike tracks
• colorAnnotations are independent of valueScale
• Vertical zooming on BedLike annotations
• Added support for aggregation of horizontal-multivec rows by passing arrays of row indices to the selectRows option. With this addition also comes the track options selectRowsAggregationMode (for specifying an aggregation function, "mean", "sum", "variance", "deviation") and selectRowsAggregationWithRelativeHeight (boolean) to determine whether rows representing groups of indices have 1-unit heights or group.length-unit heights.
• Added the JS API .on('wheel', callback) option for subscribing to mouse wheel events.

Detailed changes since v1.9.0

v1.9.0

• Support for gene annotation "filler" regions
• Clickable gene annotations
• Slightly updated gene annotation style with arrowheads at the ends
• Remove Content-Type headers when fetching genbank files
• Added the fields xRange and yRange the object returned by the JavaScript API .getLocation() method.
• Fixed blurry exported heatmap SVG graphics issue using the image-rendering CSS property.
• Enabled view-based scaling
• Left and right tracks can now be value scale locked
• Added the attributes projectionXDomain and projectionYDomain to the viewport-projection-horizontal and viewport-projection-vertical, respectively, and both to the viewport-projection-center, to support the case in which the fromViewUid attribute is undefined.
• Added the .on('createSVG') listener to the JS API, with the corresponding .off('createSVG'), for manipulating exported SVGs before they are returned.
• Added zeroValueColor as an option for the horizontal-multivec track, to specify the color mapping for zero data values.
• Track resizing events now trigger the .on('viewConfig') JS API callback.
• Allowed K and M notations when entering genomic coordinates in searchbox (e.g., "chr1:150M-155M").
• Specify raw tiles locally in the viewconf

Detailed changes since v1.8.4

v1.8.4

• Corrupted lock bug fix
• Export to SVG with no loaded tiles bug fix
• selectRows option for Horizontal Multivec Tracks

Detailed changes since v1.8.3

v1.8.3

• Added "empty" track

Detailed changes since v1.8.2

v1.8.2

• Fixed horizontal track not rendering properly in vertical position bug

Detailed changes since v1.8.1

v1.8.1

• Prettified JS code
• Added labelShowAssembly as an option to allow hiding the assembly in track label (e.g. hg19 | text)
• Added tickFormat and tickPosition options to the chromosome labels track
• Enabled the colorbar slider by adding the options colorbarPosition and colorbarBackgroundColor for the horizontal-multivec
• Added release notes to docs.
• Added support for selecting and filtering rows of the horizontal-multivec track via the selectRows option.

Detailed changes since v1.8.0

v1.8.0

• Added the option to flip 2D annotations across the diagonal
• Update heatmap docs with colorRange parameter
• Update BedLikeTrack to display strand-specific entries
• Added 'segment' style to the BedLikeTrack
• Updated default plot types when adding tracks
• When adding multiple tracks at once that have different datatype, each track is added with its default plot type. The plot type chooser is hidden.
• In HorizontalLine1DPixiTrack, make sure that this.valueScale is set when getMouseOverHtml() is called.
• VerticalRule, HorizontalRule, and CrossRule tracks included in SVG and PNG exports.

Detailed changes since v1.7.2

v1.7.2

• Refactored the scroll options and bounded into a new property called sizeMode. There are now 4 different size modes, which determine the visible height of the HiGlass instance:
  1. default: the height is given by the sum of the tracks' heights
  2. bounded: tells the HiGlass component to bind the height to the parent container by dynamically adjusting the height of center tracks.
  3. scroll: will activate scrolling by stretching HiGlass' drawing surface to the extent of parent DOM element and hiding overflowing content in the x direction and allowing to scroll when content overflows in the y direction.
  4. overflow: same as scroll except that you can't scroll. This mode is only needed when you want to dynamically switch between scrolling and pan+zooming.

Detailed changes since v1.7.0

v1.7.1

Same as v1.7.0. This is just due to a glitch at npmjs.org.

v1.7.0

• Add support for scrollable views. Activate via the option scrollable: true. Once you activate scrollable views all views are automatically zoomfixed! See http://localhost:8080/others/scrollable-container.html for an example.
• Add option(key, value) to the JS API for changing options. It supports getting all options when value is ommited and setting scrollable.
• Properly display "Loading" while loading tileset info
• Add support to ignore offscreen values for value scale locking by setting ignoreOffScreenValues: true for a lock group in locksDict.

Detailed changes since v1.6.12

v1.6.12

• Rename React lifecycle methods according to their recommendations
• Add support for borders (via the stroke, strokeWidth, strokeOpacity, and strokePos options) and outlines (via the outline, outlineWidth, outlineOpacity, and outlinePos options) to overlays. See http://localhost:8080/apis/svg.html?/viewconfs/fancy-overlays.json for an example.
• Fixed horizontal rule bug (from Slack)

Detailed changes since v1.6.11

v1.6.11

• Overlay track bug fixes
• Added minWidth and minHeight options to overlays for better guidance
• Allow viewconf JSON to override minimum track height or width defaults, when a track specifies a minHeight or minWidth parameter

Detailed changes since v1.6.10

v1.6.10

• Add API call for show track chooser (hgApi.showTrackChooser())
• Limit icon size in plot type chooser
• Add non-gzipped support to genbank-fetcher
• Better error handling for genbank fetcher

Detailed changes since v1.6.9

v1.6.9

• Enable brushing on bar, point, and 1d-heatmap tracks

Detailed changes since v1.6.8

v1.6.8

• Add infrastructure for value scale zooming
• Fixed the colors when dragging a track over a higlass display
• Added support for value scale zooming
• Added utils/track-utils to provide track functionality for use without inheritance
• Implemented a genbank data fetcher for gene annotation tracks

Detailed changes since v1.6.7

v1.6.7

• Fix #747: the tooltip value wasn't shown because of an issue related to minimizing the code
• Fix #743: the tooltip position now incorporates the scroll position
• Fix drag handle styling (typo)
• Make drag handle area (not the style) bigger so it's easier to grab

Detailed changes since v1.6.6

v1.6.6

• Fix #732: Remove the hold ALT feature as it's confusion and leads to a weird bug.
• Fix leaking dark mode setting
• Change option to activate dark theme from isDarkTheme: true to theme: 'dark'. Also, use setTheme() of the JsAPI instead of setDarkTheme() from now on.
• Copy the tile data before mutation to fix an issue when displaying the same tileset twice (once in the upper right and lower left triangle)

Detailed changes since v1.6.5

v1.6.5

• Fixed the replace track bug (where replacing a center track wouldn't do anything)

Detailed changes since v1.6.4

v1.6.4

• Truly fix #593: zoom to data extent when adding the first track to an empty view

Detailed changes since v1.6.3

v1.6.3

• Dynamically update dark theme when the options change
• Fix #722: added labelShowResolution as an option to allow hiding the [Current data resolution...] text
• Add support for missing values (NaNs) to the 1D heatmap track
• Use the new link format

Detailed changes since v1.6.2

v1.6.2

• Render horizontal-heatmap track properly in PIXI v4 and v5
• Expose pixi renderer to plugin tracks to allow them to render textures from graphics objects. (More here: https://github.com/pixijs/pixi.js/issues/5394)

Detailed changes since v1.6.1

v1.6.1

• Fix visual glitches with the new Modal when run in higlass-app
• Really fix #651: set correct namespace for SVG exports
• Treat tilesetInfo.mirror_tiles = false as a falsy value
• Fixed: Save and Close in the ViewConfigEditor works properly

Detailed changes since v1.6.0

v1.6.0

• Add an option to restrict the extent of central heatmaps to the upper-right or lower-left corner to enable comparison of two heatmaps in the center. Run npm start and see http://localhost:8080/apis/svg.html?/viewconfs/diagonal-split-heatmap.json for an example
• Updated pixi.js to version 5. In your html files you need to replace the previous PixiJS loader with <script crossorigin src="https://unpkg.com/pixi.js@5/dist/pixi.min.js"></script> (or <script crossorigin src="https://unpkg.com/pixi.js-legacy@5/dist/pixi-legacy.min.js"></script> if you want to use the Canvas renderer)
• Add a dialog to directly edit the view config in the browser
• Replace ReactBootstrap modal with custom modal to not rely on Bootstrap and support Jupyter
• Updated pub-sub-es to version 1.2.1 to fix a bug in the shorthand event unsubscription
• Added an example of a map overlay
• Support semi-transparent colormaps through RGBA colors
• Update Mapbox endpoint. See http://localhost:8080/others/mapbox.html for an example.
• Improve performance of the mousemove-related event handling
• Remove unused properties from the exported view config
• Improve performance of tiles fetching through a combination of throttling and debouncing
• Fix a minor visual glitch with the positioning of track-related divs
• Fix OSM track to avoid CORS issues in Chrome and allow setting minPos to 0
• Fix #648: Auto select and copy URL when exporting a view by link
• Fix #647: Shows correct URL when specifying an absolute URL as exportViewUrl in the viewconf
• Fix #651: set correct namespace for SVG exports
• Fix #593: zoom to data extent when adding the first track to an empty view

Detailed changes since v1.5.8

v1.5.8

• Fix a value scale syncing bug
• Update the docs

Detailed changes since v1.5.7

v1.5.7

• Fix #637 - SVG export fill color doesn't match what is selected
• Switch to nearest neighbor interpolation for horizontal heatmaps

Detailed changes since v1.5.8

v1.5.6

• Allow any horizontal track to also be placed on the left or right

Detailed changes since v1.5.8

v1.5.5

• Fixed #612: resolved an issue with caseinsensitive chromosome names
• Destroy heatmap sprites and axis texts to mitigate memory leak

Detailed changes since v1.5.4

v1.5.4

• Fix the multiple component passive event issue by replacing the dom-event.js handlers with a class so that each component maintains its own context

Detailed changes since v1.5.3

v1.5.3

• Let HorizontalLineTracks look up tileset_info.tile_size and tileset_info.bins_per_dimension
• Specify default track types directly in showAvailableTrackTypes API
• Updated the docs deploy directory
• Updated the javascript API example to include a full working html page
• Use default height for new tracks rather than min height. Fixes newly added gene annotations so that they show names without having to be resized
• Fixed bug that was causing overlay tracks to not appear
• Fixed horizontal-vector-heatmap error thrown bug by padding incomplete incoming data arrays

Detailed changes since v1.5.1

v1.5.1

• Fixed UI hanging on mouseover of zoomed out matrix bug
• Fixed #588: horizontal heatmap zoom limit bug
• Reset value scale locks when new viewconf is added
• Added a default track type for the chromsizes datatype
• Fixed drag handler pubSub reference
• Fixed #596: scrolling while zooming bug introduced in latest chrome

Detailed changes since v1.5.0

v1.5.0

• Allow sharing the mouse position globally. See docs/examples/others/global-mouse-position.html for an example.
• Allow disabling the change of views and tracks separately by setting viewEditable: false and tracksEditable: false in your view config.
• Added ability to define label margins. See docs/examples/viewconfs/label-margin.json for an example.
• Make view spacing adjustable via initialization options. See /docs/examples/others/adjust-view-spacing.html for an example.
• Add a new option to tracks that support axis: axisMargin to add some margin to an axis. See docs/examples/viewconfs/axis-margin.json for an example
• Add a new option to BarTrack for drawing a demarcation line at the bottom of the track, i.e., at the zero value. See /apis/svg.html?/viewconfs/bar-zero-line.json for an example.
• Fixed an issue with small offsets when exporting bar tracks to SVG
• Fixed an issue where bars in a BarTrack related to values higher than valueScaleMax were not drawn.
• Fixed an issue with hgApi.setTrackValueScaleLimits
• Fix #291: allow web page scrolling when zoomFixed is set to true
• Fix #578: BarTrack SVG export overplotting error.
• Fix #584: Reset viewport is broken

Detailed changes since v1.4.2

v1.4.2

• Fix #568, #569

v1.4.1

• Allow users to choose adding the chromosome grid overlay from the Add Track Dialog when selecting a cooler file.
• Expose version from hglib. E.g., window.hglib.version

v1.4.0

• Add constIndicators as an option to 1D tracks for displaying a visual indicator (e.g., a line) at a constant value.
• Added [glyph-color] as the default option for line and bar tracks
• Add new public event cursorLocation. See docs/examples/apis/cursor-location.html for an example.
• Extend mouseMoveZoom event to support 1D data tracks.
• Expose D3 libraries to plugin tracks
• Overlay tracks now properly allow for extent to include multiple ranges.
• Overlay tracks can now optionally have extent ranges configured as a 4-tuple, separating x ranges from y ranges

v1.3.1

• Clear mouse position indicator when leaving the root dom element, on blurring the window, and when no track is hovered

v1.3.0

• Changed defaultOptions to defaultTrackOptions in the hglib.viewer options.
• Added TiledPixiTrack.on event handler to listen to data changes
• Added several API endpoints: getComponent(), setAuthHeader(), getAuthHeader(),
• Added export of several utility functions: waitForJsonComplete(), waitForTilesLoaded(), waitForTransitionsFinished(), mountHGComponent(), getTrackObjectFromHGC()
• Added the ability to specify default track options through the API
• Added nesting to the tileset finder so that tilesets can be grouped together into categories
• Added the axisLabelFormatting option to 1d quantitative tracks
• Added TiledPixiTrack.on event handler
• Added getTrackObject to exports
• Added support for overlay tracks
• Minor bug fix wherein valueScaleMin and valueScaleMax weren't used when set to 0
• Added support for click event handling of 1D and 2D annotations from 1d-annotation and chromosome-2d-annotations tracks
• Cloned views split vertically first (#259)
• Change component height when a new viewconf is passed in
• Add a fudge factor to ensure that the entire view is shown in the grid layout
• Refactored the pub-sub service to avoid implicit global event listening
• Fix a minor visual glitch in the gene annotation track
• Expose mix() from mixwith to plugin tracks
• Support different aggregation modes (mean, min, max, std) for bigWig files
• Changed defaultOptions to defaultTrackOptions in the hglib.viewer options.
• Clear mouse position indicator when leaving the root dom element, on blurring the window, and when no track is hovered
• Fix several issue with SVG export
• Minor bug fix wherein valueScaleMin and valueScaleMax weren't used when set to 0
• Fix #401
• Fix #395
• Fix #360
• Support different aggregation modes (mean, min, max, std) for bigWig files

v1.2.8

• Added editable as a possible option to hglib.viewer()
• Enabled arbitrary tile resolution in HeatmapTiledPixiTrack. It just needs to receive bins_per_dimension in the tileset info. Otherwise it defaults to 256.

v1.2.6

• Fixed trackSourceServer export
• Fixed BedLikeTrack errors being thrown

v1.2.5

• Fix remote viewConf loading in HiGlassComponent

v1.2.4

• Fix #322
• Fix missing update of the value scale upon rerendering
• Fix absToChr and chrToAbs of the ChromInfo API
• Fixed a nasty rendering bug in the chrom labels track

v1.2.3

• Fixed line inversion issue (#268)
• Fixed fetched area size mismatch issue on mouseover
• Added mouseover text to UI elements
• Upgraded to webpack 4
• Started building hglib.js and hglib.min.js
• Support for searching for gene names with dashes
• Sort tilesets alphabetically (#256)
• Fixed zoom linking issues (#251, #76)

v1.2.1 and v1.2.2

• Accidental releases. Please ignore.

v1.2.0

• Add 1D heatmap track (#303): Alternative visual representation of 1D bigwig tracks. See https://github.com/higlass/higlass/pull/303 and https://github.com/higlass/higlass/blob/develop/docs/examples/1d-heatmap-track.html for an example.

• Add fixing y-scale of 1D data tracks (#297). See https://github.com/higlass/higlass/pull/297 and https://github.com/higlass/higlass/blob/develop/docs/examples/api-set-track-value-scale-limits.html for an example.
• Add JS-API for resetting the viewport back to the initial x and y domains in the viewconfig (#289)
• Add JS-API for adjusting the margin of the HiGlass instance (#286). See https://github.com/higlass/higlass/pull/286 for an example.
• Add JS-API for getting the min and max value of a track (#298). See https://github.com/higlass/higlass/blob/develop/docs/examples/api-get-min-max-value.html for an example.
• Enhance bed track (#278): support value encoding as the y offset or color. See https://github.com/higlass/higlass/pull/278 for an example.
• Enhance gene annotation track (#314): See https://github.com/higlass/higlass/pull/314 and https://github.com/higlass/higlass/blob/develop/docs/examples/gene-annotations.html for an example.

• Enhance chrom label track (#305): add support for adjusting the font size, font alignment, and font outline to use space more economically. See https://github.com/higlass/higlass/pull/305 and https://github.com/higlass/higlass/blob/develop/docs/examples/chromosome-labels.html for an example.

• Enhance bar track (#304): add color and gradient encoding plus diverging tracks. See https://github.com/higlass/higlass/pull/304 and https://github.com/higlass/higlass/blob/develop/docs/examples/bar-track-color-range.html for an example.

• Expose absToChr and chrToAbs API on ChromInfo (#283 and #307)
• Upgrade to React v16.5
• Removed numjs (#320)
• Update tool tip appearance (#309)
• Make resize handle fade out and in upon mouse enter of a draggable div
• Enlarge resize handle upon mouse enter
• Remove all tracks from the 'whole' window when clearing the view
• Fix viewport projection issue when there are vertical and horizontal rules
• Fix colorbar positioning bug
• Fix #317 (moving gene positions)
• Fix #263
• Fix #245: track type selection bug
• Fix #262: zoom to data extent issue

v1.1.5

• Merge'd Chuck's PR for adding 'same-origin' to fetch request headers
• Fixed a bug where a view without a layout is created with a width of 1

v1.1.4

• Fix the checkAllTilesetInfoReceived function so that it ignores left and top axis tracks
• First release to be registered with Zenodo

v1.1.3

• Add z-index to mouseover div so that it's not hidden behind other elements

v1.1.2

• Inline the SVG styles so they aren't overwritten by other elments on the page
• Inline TrackControl svg styles so they aren't overwritten by page css settings
• Clear gene annotation graphics before redrawing

v1.1.1

• Fixed export track data bug in heatmaps that are not combined tracks

v1.1.0

• Check whether the tileset_info specifies that the tiles should be mirrored
• Added data export feature
• Added showMousePosition and showMouseTooltip to horizontal-bar-track

v1.0.4

• Zoom through the viewport projection

v1.0.3

• Fixed cross rule bug

v1.0.2

• Added vertical divergent bar tracks
• Fixed export in SVG
• Fix mouseover error when trackrenderer hasn't been initialized yet
• Added zoomFixed option to the top level of the viewconf
• Use transpiled version of mixwith.js
• Add options to change the background of the label and colorbar

v1.0.1 (2018-06-14)

• Fixed background export in SVG
• Turned off line mouseover by default

v1.0.0-alpha.12

• Fixed long loading bug on zoomed in genes

v1.0.0-alpha.11

• Fixed gene stretching issues

v1.0.0-alpha.10

• Fixed background rendering after resizing
• Fixed viewconf export link (use state.viewconf vs props.viewconf)

v1.0.0-alpha.9

• Fixed lock value scales

v1.0.0-alpha.8

• Fixed tooltip scrollbar appearance
• Fixed context menu appearing issue

v1.0.0-alpha.7

• Fixed scrolling bug when multiple higlass components are on a single page
• Fixed hover bug in combined tracks

v1.0.0-alpha

• Added triangles to genes
• Preliminary authentication support
• Added track for displaying gigapixel images
• Added GeoJSON track and updated OSM track
• Added mouseMoveZoom event to public API
• Fixed and extended pubSub module
• Added flexible per-track crosshair
• Fixed and robustified range selection API
• Display error message on error
• Don't error when displaying menus when invalid track type is entered
• Added an endpoint for sharing view configs as a link (shareViewConfigAsLink()) and exporting them as png and svg (get('png' || 'svg'))
• Simplified hglib API
• Updated third-party libs to get rid of deprecation warnings for React v16
• Fixed small bug in placing rules
• Display error when failing to retrieve tilesetInfo

• Added support for cross-section tracks

• Rendering improvements

v0.10.22 (2018-02-22)

• Added options to change the fill color of bedlike tracks

v0.10.21 (2018-02-21)

• Exposed the ChromosomeInfo structure as part of the hglib API

v0.10.20 (2018-02-??

• Rendering improvements

v0.10.20 (2018-02-20)

• Fixed api variable in HiGlassComponent
• Fixed relToAbsChromPos so that it converts locations to numbers before adding
• Added strokeWidth as an option to the viewport projection track

v0.10.19 (2018-02-11)

• Fixed the 2D chromosome labels track

v0.10.18 (2018-02-11)

• Fixed Horizontal2DTilesTrack

v0.10.16 (2018-

• Don't show the "Strange tileData" warnings
• Pegged bootstrap to version 3.3.7

v0.10.16 (2018-02-01)

• Fixed a bug during active range selection when the select mouse tool is deactivated

v0.10.15 (2018-01-30)

• Added the vertical bed-like track

v0.10.13 (2018-01-25)

• Added the multivec track

v0.10.12 (2018-01-21)

• Fixed pseudocounts in linear-scaled heatmaps

v0.10.12 (2018-01-20)

• Fixed get scale bug

v0.10.11 (2018-01-17)

• Fixed non-draggable views bug

v0.10.10 (2018-01-17)

• Default to log scaling if there are negative values
• Fixed the custom colormap
• Fix the gene annotations color changing
• Fixed two regressions regarding the viewport projections

v0.10.9 (2018-01-13)

• Skipping a version because the latest version wasn't specified in package.json

v0.10.8

• Skipping a version because the latest version wasn't specified in package.json

v0.10.7 (2018-01-13)

• Show current data resolution in tiled sets containing raw resolutions rather than zoom levels

v0.10.6 (2017-12-28)

• Load ResizeSensors after the element is attached to the DOM tree
• Added DivergentBarTrack
• Fixed submenu hiding bug

v0.10.5 (2017-12-27)

• Fixed bug in TrackRenderer.setUpInitialScales where updating the view with new equivalent initial domains and different dimensions led to the view being misplaced
• Added z-index to popup menus

v0.10.4 (2017-12-16)

• Fixed a bug in zoomToData
• New API call for setViewConfig
• New API call for zoomToDataExtent

v0.10.3 (2017-12-13)

• Don't include a colon if the port is 80
• Added an option to clear the view
• Exclude NaN values when setting the valueScale
• Fixed bug related to displaying empty matrix tiles

v0.10.2 (2017-12-12)

• Fixed a bug in loading tileset info that isn't there
• Better error handling on internal server error
• Removed functionless menu item

v0.10.1 (2017-12-05)

• Fixed bug in Bedlike tracks that don't have a header

v0.10.0 (2017-12-05)

• Change track type from the config menu
• Initial framework for divided by tracks
• Y-positioned bed-like tracks

v0.9.16 (2017-

• Fixed undefined error when toggling genome position search box

v0.9.15 (2017-11-22)

• Fixed bug where newly selected annotations weren't being used
• Added the hideHeader option
• Added a warning for malformed gene annotations
• Free up webgl renderer resources when unmount
• Minor CSS cleanup
• Fix resizing bug that appears after closing a view
• Warn if there are no track source servers specified in the viewconf

v0.9.14 (2017-11-11)

• Show labels on bar chart

v0.9.13 (2017-11-09)

• Fixed gene position searching regression

v0.9.12 (2017-11-08)

• Fix inter-chromosomal searches (chr1-chr2)

v0.9.11 (2017-11-08)

• Fix gene annotation coloring bug
• Fix menu clash error that occurs when a center track is specified without a combined track
• Zoom into entire chromosomes by just entering its name

v0.9.10 (2017-11-01)

• Fixed d3 brush Error: attribute height: Expected length, "Infinity"
• Fixed scale initialization error
• Added back heatmap value scaling
• Fixed horizontal heatmap multires tile loading
• Better point export

v0.9.9 (2017-11-01)

• Fix SVG bar chart export
• Fixed network error on SVG export again (from v0.8.44)

v0.9.8 (2017-10-31)

• Switch back to minified build

v0.9.7 (2017-10-31)

• Initialize scales when viewconfig is loaded rather than on handleScalesChanged

v0.9.6 (2017-10-31)

• Faulty build (package.json wasn't there)

v0.9.5 (2017-10-31)

• Fix visual clash of the center track's context menu and the colormap
• Make visualization of 2D annotations more flexible: stroke width and fill / stroke opacity can be changed
• Create debug output files

v0.9.4 (2017-10-26)

• Reintroduced value scale serialization fix
• Fixed HorizontalHeatmapExport
• Added a minimum width to 2D annotations
• Added SVG export for 2d-rectangle-domains track

v0.9.3 (2017-10-23)

• Removed console log statement

v0.9.2 (2017-10-23)

• Fixed the build script to copy hglib.css rather than style.css

v0.9.1 (2017-10-23)

• Add support for vertical bar tracks
• Fixed .travis.yml release issue

v0.9.0 (2017-10-21)

• Add 1D and 2D range selection
• Add support for SASS
• Add support for CSS Modules
• Update visuals of the context menu and view header
• Integrate search bar into view header
• Add ESLint and adhere to consistent code style
• (Fix #135) - Colorbar moves with the track when it's being resized
• (Fix #126) - Gene annotations shouldn't overlap on vertical tracks anymore
• Keep track controls visible if config menu is active
• Show child menus above the parent if there isn't enough space on the bottom
• Add port number when exporting viewconfs from a non-standard port
• Support arbitrary resolutions in heatmaps

v0.8.44

• Redraw TiledPixiTracks after the tileset info has been received
• Remove value scale locks on handleCloseTrack
• Check that tiledPlot is defined in createSVG to fix the export failing when there's two side-by-side by views created after closing one
• Fixed the "Failed: network error" issue in chrome by changing the "download" function in utils.js

v0.8.43

• More fixes for SVG output for bedlike tracks

v0.8.42

• Fixed SVG output for bedlike tracks

v0.8.41

• Fixed chromosome grid color bug
• Fixed chromosome grid loading with many values bug

v0.8.40

• Fixed value scale locking bug

v0.8.37

• Fixed center track label background oddness (#144)

v0.8.36

• (fix #146) Fixed value scale locking serialization bug
• Fixed gene annotation SVG export
• Fixed chromosome ticks SVG export

v0.8.35

• Fixed colorbar hiding bug (Issue #131)

v0.8.34

• Fixed horizontal heatmap loading after the adjustable color scale changes
• Fixed vertical heatmap loading
• Fixed vertical heatmap colorscale brush in LeftTrackModifier

v0.8.33

• Removed the outside colorbar labels option (it's a little ambiguous on the right side since the labels will be adjacent to the other axis elements.

v0.8.32

• Removed tests from package.json so that build completes (tests fail on travis for some reason)

v0.8.31

• Add a color limit selection to the Heatmap track in HiGlass

v0.8.30

• Cherry picked the BedLikeTrack from the circle branch

v0.8.28

• Fixed dependencies (peer and normal)
• Fixed other minor issues with package.json

v0.8.27

• Fixed bug wher the "Loading" sign remained with 1D point tracks

v0.8.26

• Different mapbox style options

v0.8.25

• Hidden OSM tiles
• Customizeable osm width

v0.8.24

• Major performance improvements for Gene annotations and horizontal points
• Fixed bug in searching for genome positions with a space at one of the ends
• Added the OSM tiles

v0.8.23

• Don't show chromosome sizes as a separate track

v0.8.22 - 2017-07-13

• Safari add track bug fix
• Backwards compatibility on selectable chromosome axis tracks

v0.8.21 - 2017-07-10

• Fixed the default transformation for horizontal tracks

v0.8.20 - 2017-07-10

• Fix label display

v0.8.19 - 2017-07-10

• Added the ability to select different transformations

v0.8.18 - 2017-06-29

• Fixed custom colormap picker
• Fixed overlayed track addition on double click

v0.8.17 - 2017-06-28

• Performance improvements

v0.8.16 - 2017-06-27

• Fixed a regression where closing views didn't remove the associated PIXI Components
• Increased the drag timeout time to 5 seconds

v0.8.15 - 2017-06-26

• Lowered the maximum number of tiles retrieved at once to 20

v0.8.14 - 2017-06-26

• Increase the maximum number of tiles retrieved at once to 40

v0.8.13 - 2017-06-26

• Option to draw borders around tracks
• Option to change the stroke, fill colors and opacity of the horizontal-2d-rectangle-domains track

v0.8.12 - 2017-06-26

• Hide overflow track handles

v0.8.11 - 2017-06-26

• Fixed double click track addition bug
• Mask view boundaries so that when the tracks are too large to fit inside, they don't overflow outside of their view
• Added favicon

v0.8.10 - 2017-06-25

• Multiple tileset selection
• Disabled zooming on scrolling fix

v0.8.9

• Make sure that the zoomable div matches the size of the container

v0.8.8 - 2017-06-20

• Don't start zooming when scrolling into a HGC

v0.8.7 - 2017-06-18

• Decreased the maximum colorbar height
• Made the draggable div handles more transparent
• Lowered the minimum height for chromosome axes

v0.8.6 - 2017-06-18

• Fixed a bug where the HG Component would automatically and indefinitely increase in size

v0.8.5 - 2017-06-16

• Fixed view linking bug (regression)
• Added horizontal and vertical 2D domains tracks

v0.8.4 - 2017-06-12

• Include a limit in the tilesets query so that all results are returned

v0.8.3 - 2017-06-06

• Fixed a regression where adding new tracks doesn't work

v0.8.2 - 2017-06-01

• Move hglib.css to dist/styles rather than dist/

v0.8.1 - 2017-06-01

• Changed package.json to create hglib.css rather than style.css

v0.8.0 - 2017-06-01

• Switched to webpack 2
• Various warning fixes in the code
• Pull chromsizes from the tilesets table instead
• Remove the chroms table and app

v0.7.3 - 2017-05-23

• Added stroke width as a property of line tracks
• Fixed view layout bug caused by the "i" member of the layout not matching the view's uid
• Fixed resizing so that vertical changes get handled immediately

v0.7.2

• Added purple and turquoise colors
• Added an option to control the label opacity

v0.7.1

• Added horizontal and vertical track viewport projections
• Bug fix where assembly name gets removed from track label

v0.7.0

• Added an assembly selector to the GenomePositionSearchBox
• Prefix track names with their assembly

v0.6.9

• Lower the default resolution of lines for performance reasons
• Added outsideLeft, outsideRight, outsideTop and outsideBottom as available axis positions

v0.6.8

• Component sizes are adjsuted on component load
• Genome position search box styling is set to not have a bottom margin

v0.6.7

• Unbounded functionality to increase the size of the layout if new tracks are added which increase its size
• Configurable track label background opacity
• Fixed: vertical colorbar label mirroring

v0.6.6

• Bug fix: closing a track which had a value scale lock with another track now works

v0.6.5

• Bug fix: tracks rendered with locked scale, rather than just the colorbar
• Bug fix: locked line scales
• Bug fix: assorted other track locking, scale and colorbar bugs

v0.6.4

• Added value scale locking
• Fixed bug where newly added heatmaps didn't render (syncTrackObjects needs to call applyZoomTransform)
• Fixed bug where new chromosome axis didn't appear after being added - Had to call animate after the chromosome info was received

v0.6.3

• Added colorbar for Heatmaps
• Draw scales on the outside of the linear tracks
• Added the SquareMarkerTrack

v0.6.2

• Scale tracks from minimum to maximum value, rather than starting at 0

v0.6.1

• Fixed a minor issue with chromosome labels not being exported

v0.6.0

• Automatically draw the 2D grid after the data is loaded
• Add animated zoom transitions
• Add public BEDPE-like API to navigate to a given location
• SVG export
• Testing using Karma
• (Might have been in a different release) Default to interpolation-less rendering

v0.5.16

• Fixed resizing bug

v0.5.15

• Added mm9 chromosome labels
• Draw chromosome labels on reload
• Take name from track options

v0.5.14

• Revert the initialXDomain changes Fritz introduced because they were causing issues with faithful reproduction of viewconfs
• Change 'tilesetInfo not loaded message' to 'loading...' until we either get an error or the tileset is loaded
• Omit certain fields from JSON export (HiGlassComponenent.getViewsAsString)

v0.5.12

• Fixed export viewconfig link bug

v0.5.11

• Added the fall colormap and made it the default

v0.5.10

• Fix Chromosome2DAnnotations not being drawn by calling draw after the ChromosomeInfo is loaded
• Zoom to the currently visible data
• Use the minimum position to load data that is not located at the origin
• Viewconf downloads work on Firefox
• Alert when trying to project a viewport on the same view
• Resize handle positions fixed in Firefox
• Track config button icons fixed in Firefox
• Only redraw in timedUpdate if track positions have changed
• Fixed top and left axis not appearing bug
• Fixed chromosome horizontal labels not appearing
• Show minValue pixels by scaling from minValue to maxValue + minValue and adding minValue to each pixel
• Fix viewport projection error when new viewconfig is passed

v0.5.9

• Labels outside of the bounds of a track
• Label colors

v0.5.8

• A host of performance improvements

v0.5.7

• Empty accidental release

v0.5.6

• Add log scaling to line tracks
• Add colors to line tracks
• Add width option to 2D grid
• Add color option to 2D grid

v0.5.5

• Add per-view zoomFixed settings
• Added configurable viewport projection colors (projectionFillColor, projectionStrokeColor)
• Added an empty .npmignore to prevent it from excluding the dist/ directory specified in the .gitignore
• Enhance 2D annotations by supporting RGBA, fill and stroke-dependent coloring, and locus-wise min width / height definitions
• Remove builds. Use NPM

v0.5.4

• Fixed bug related to the selection of the plot type
• Update existing tracks before adding new ones in syncTrackObjects
• Removed the "Move up" menu item
• Deep copy incoming viewconfs so that changing them outside of the component leads to an update
• Added onLocationChanged event listener

v0.5.3

• Forgot to bump the version number in 0.5.2

v0.5.2

• Don't draw data that extends beyond the end of the assembly
• Fixed bug where data was being hidden in empty (all 0) tiles - Changed minVisibleValue and maxVisibleValue in TiledPixiTrack
• Label the horizontal and vertical line tracks by default

v0.5.1

• Configurable gene annotation colors
• Added chromosome annotations tracks for programmatically addeable annotations
• Fixed the 'Cannot read property 0 of undefined' bug when tileset info is inaccessible
• Remove track resize handles when the component isn't editable
• Fix bug associated with setting a new initial[X/Y]Domain where the cumulativeCenterOffset wasn't being reset
• Bug fix where if a view doesn't have a uid we should assign it one

v0.5.0

• Default to 12 columns
• Display a warning if tileset info isn't found
• Use 16bit floats for heatmap data

v0.4.40

• Remove default colormap from viewconfig

v0.4.39

• Switch cog and close buttons

v0.4.33

• New header colors

v0.4.32

• Reduced the number of tiles requested by the horizontal heatmap track
• Removed console log statements

v0.4.31

• Fixed regression and compatibility change with new zoom and location locking
• Fixed regression in the selection dragging

v0.4.30

• Added a minimum width to left-axis so that it doesn't only show the last two digits by default

• Added horizontal and vertical heatmaps

• Styling changes for the Configure track controls
• Fixed the bug with AddTrackMenu cancel button turning black by properly increasing the number of visible tilesets in TilesetFinder
• Added options to allow flipping horizontal and vertical charts
• Fixed NaN prefix bug
• Fixed invalid negative value attributes for bug

v0.4.29

• Moved default heatmap information to lower right hand corner
• Fixed a bug which distorted the view when initialized with an initial X scale and Y scale
• Added white to red, white to green and white to blue scales
• Added axes for the 1D tracks
• Took the ID out of the view header
• Added a white border behind the track controls

v0.4.28

• Fixed critical regression where track replacement wasn't working because newly created tracks didn't have their options set
• Fixed a regression where track movement wasn't working because TiledPlot wasn't being updated
• Increase the size of the tileset selector

v0.4.27

• Changed config.js Chromosome Labels to Chromosome Axis
• Fixed default option setting so that it doesn't override provided options
• Adding zoom limit option to heatmap
• Add current resolution to the track label
• Fixed regression caused by "Fast redraw by tiling commit"
• Hitting enter in the genome position search box initiates a search

v0.4.26

• Fixed close button

v0.4.25

• Fractional zoom lock
• Faster config menu loading
• Faster track addition by limiting the udpates of TiledPlot (using shouldComponentUpdate)

v0.4.21

• Chromosome grid positions start at position 1
• Export link includes 'app'

v0.4.20

• Changed tile API location to use included server value rather than prepending '//'

v0.4.19

• Removed dist directory from .gitignore

v0.4.18

• Use production react in the build
• Added dist to .gitignore

v0.4.17

• Updated default view config
• Wider ticks

v0.4.16

• Fritz's public API

v0.4.15

• Fritz's lazy animation
• Fritz's public API
• Minimum height for tracks can be specified in track type definition in config.js
• New chromosome 2D grid (for hg19)
• New chromosome 1D axis (for hg19)
• New chromosome horizontal axis (for hg19)