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PileupRenderer

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

Source file​

plugins/alignments/src/PileupRenderer/configSchema.ts

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',
    }