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PileupRenderer

Note: this document is automatically generated from configuration objects in our source code. See Config guide for more info

Also note: this document represents the config API for the current released version of jbrowse. If you are not using the current version, please cross reference the markdown files in our repo of the checked out git tag

Source code

GitHub page

Docs​

PileupRenderer - Slots​

slot: color​

default magenta here is used to detect the user has not customized this

color: {
      type: 'color',
      description: 'the color of each feature in a pileup alignment',
      defaultValue: '#f0f',
      contextVariable: ['feature'],
    }

slot: orientationType​

orientationType: {
      type: 'stringEnum',
      model: types.enumeration('orientationType', ['fr', 'rf', 'ff']),
      defaultValue: 'fr',
      description:
        'read sequencer orientation. fr is normal "reads pointing at each other ---> <--- while some other sequencers can use other options',
    }

slot: displayMode​

displayMode: {
      type: 'stringEnum',
      model: types.enumeration('displayMode', [
        'normal',
        'compact',
        'collapse',
      ]),
      description: 'Alternative display modes',
      defaultValue: 'normal',
    }

slot: minSubfeatureWidth​

minSubfeatureWidth: {
      type: 'number',
      description:
        'the minimum width in px for a pileup mismatch feature. use for increasing/decreasing mismatch marker widths when zoomed out, e.g. 0 or 1',
      defaultValue: 1,
    }

slot: maxHeight​

maxHeight: {
      type: 'integer',
      description: 'the maximum height to be used in a pileup rendering',
      defaultValue: 1200,
    }

slot: maxClippingSize​

maxClippingSize: {
      type: 'integer',
      description: 'the max clip size to be used in a pileup rendering',
      defaultValue: 10000,
    }

slot: height​

height: {
      type: 'number',
      description: 'the height of each feature in a pileup alignment',
      defaultValue: 7,
      contextVariable: ['feature'],
    }

slot: noSpacing​

noSpacing: {
      type: 'boolean',
      description: 'remove spacing between features',
      defaultValue: false,
    }

slot: largeInsertionIndicatorScale​

largeInsertionIndicatorScale: {
      type: 'number',
      description:
        'scale at which to draw the large insertion indicators (bp/pixel)',
      defaultValue: 10,
    }

slot: mismatchAlpha​

mismatchAlpha: {
      type: 'boolean',
      defaultValue: false,
      description: 'Fade low quality mismatches',
    }