@jbrowse/plugin-alignments 1.5.8 → 1.6.2

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Files changed (27) hide show
  1. package/dist/BamAdapter/BamAdapter.d.ts +5 -0
  2. package/dist/BamAdapter/BamSlightlyLazyFeature.d.ts +1 -2
  3. package/dist/CramAdapter/CramAdapter.d.ts +16 -5
  4. package/dist/LinearAlignmentsDisplay/models/model.d.ts +2 -1
  5. package/dist/LinearPileupDisplay/model.d.ts +28 -6
  6. package/dist/LinearSNPCoverageDisplay/models/model.d.ts +3 -0
  7. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +1 -0
  8. package/dist/plugin-alignments.cjs.development.js +557 -346
  9. package/dist/plugin-alignments.cjs.development.js.map +1 -1
  10. package/dist/plugin-alignments.cjs.production.min.js +1 -1
  11. package/dist/plugin-alignments.cjs.production.min.js.map +1 -1
  12. package/dist/plugin-alignments.esm.js +557 -346
  13. package/dist/plugin-alignments.esm.js.map +1 -1
  14. package/package.json +3 -3
  15. package/src/BamAdapter/BamAdapter.ts +56 -35
  16. package/src/BamAdapter/BamSlightlyLazyFeature.ts +18 -25
  17. package/src/BamAdapter/configSchema.ts +2 -2
  18. package/src/CramAdapter/CramAdapter.ts +105 -91
  19. package/src/CramAdapter/configSchema.ts +5 -1
  20. package/src/LinearAlignmentsDisplay/models/model.tsx +4 -3
  21. package/src/LinearPileupDisplay/configSchema.ts +3 -3
  22. package/src/LinearPileupDisplay/model.ts +8 -7
  23. package/src/LinearSNPCoverageDisplay/models/configSchema.ts +1 -5
  24. package/src/LinearSNPCoverageDisplay/models/model.ts +3 -2
  25. package/src/PileupRenderer/PileupRenderer.tsx +5 -3
  26. package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +5 -0
  27. package/src/index.ts +22 -15
package/src/LinearSNPCoverageDisplay/models/configSchema.ts CHANGED
@@ -39,11 +39,7 @@ export default function SNPCoverageConfigFactory(pluginManager: PluginManager) {
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  description: 'draw upside down',
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  defaultValue: false,
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  },
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- maxDisplayedBpPerPx: {
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- type: 'number',
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- description: 'maximum bpPerPx that is displayed in the view',
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- defaultValue: 100,
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- },
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+
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  headroom: {
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  type: 'number',
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  description:
package/src/LinearSNPCoverageDisplay/models/model.ts CHANGED
@@ -131,9 +131,10 @@ const stateModelFactory = (
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  },
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  renderProps() {
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+ const superProps = superRenderProps()
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  return {
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- ...superRenderProps(),
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- notReady: !self.ready || !this.modificationsReady,
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+ ...superProps,
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+ notReady: superProps.notReady || !this.modificationsReady,
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  filters: self.filters,
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  modificationTagMap: JSON.parse(
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  JSON.stringify(self.modificationTagMap),
package/src/PileupRenderer/PileupRenderer.tsx CHANGED
@@ -682,11 +682,13 @@ export default class PileupRenderer extends BoxRendererType {
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  const baseColor = colorForBase.deletion
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  ctx.fillStyle = baseColor
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  ctx.fillRect(leftPx, topPx, widthPx, heightPx)
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- if (widthPx >= charWidth && heightPx >= heightLim) {
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+ const txt = `${mismatch.length}`
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+ const rect = ctx.measureText(txt)
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+ if (widthPx >= rect.width && heightPx >= heightLim) {
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  ctx.fillStyle = theme.palette.getContrastText(baseColor)
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  ctx.fillText(
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- mbase,
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- leftPx + (widthPx - charWidth) / 2 + 1,
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+ txt,
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+ leftPx + (rightPx - leftPx) / 2 - rect.width / 2,
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  topPx + heightPx,
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  )
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  }
package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts CHANGED
@@ -125,6 +125,11 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
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  }, opts.signal)
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  }
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+ async estimateRegionsStats(regions: Region[], opts?: BaseOptions) {
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+ const { subadapter } = await this.configure()
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+ return subadapter.estimateRegionsStats(regions, opts)
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+ }
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+
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  async getRefNames(opts: BaseOptions = {}) {
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  const { subadapter } = await this.configure()
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  return subadapter.getRefNames(opts)
package/src/index.ts CHANGED
@@ -60,12 +60,15 @@ export default class AlignmentsPlugin extends Plugin {
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  const regexGuess = /\.cram$/i
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  const adapterName = 'CramAdapter'
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  const fileName = getFileName(file)
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- if (regexGuess.test(fileName) || adapterHint === adapterName) {
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- return {
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- type: adapterName,
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- cramLocation: file,
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- craiLocation: index || makeIndex(file, '.crai'),
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- }
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+ const obj = {
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+ type: adapterName,
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+ cramLocation: file,
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+ craiLocation: index || makeIndex(file, '.crai'),
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+ }
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+ if (regexGuess.test(fileName) && !adapterHint) {
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+ return obj
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+ } else if (adapterHint === adapterName) {
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+ return obj
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  }
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  return adapterGuesser(file, index, adapterHint)
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  }
@@ -84,15 +87,19 @@ export default class AlignmentsPlugin extends Plugin {
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  const adapterName = 'BamAdapter'
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  const fileName = getFileName(file)
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  const indexName = index && getFileName(index)
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- if (regexGuess.test(fileName) || adapterHint === adapterName) {
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- return {
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- type: adapterName,
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- bamLocation: file,
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- index: {
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- location: index || makeIndex(file, '.bai'),
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- indexType: makeIndexType(indexName, 'CSI', 'BAI'),
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- },
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- }
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+
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+ const obj = {
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+ type: adapterName,
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+ bamLocation: file,
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+ index: {
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+ location: index || makeIndex(file, '.bai'),
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+ indexType: makeIndexType(indexName, 'CSI', 'BAI'),
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+ },
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+ }
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+ if (regexGuess.test(fileName) && !adapterHint) {
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+ return obj
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+ } else if (adapterHint === adapterName) {
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+ return obj
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  }
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  return adapterGuesser(file, index, adapterHint)
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  }