@jbrowse/plugin-alignments 2.4.2 → 2.5.0

package/src/LinearPileupDisplay/model.ts

@@ -57,6 +57,13 @@ const rendererTypes = new Map([
 
 type LGV = LinearGenomeViewModel
 
+export interface Filter {
+  flagInclude: number
+  flagExclude: number
+  readName?: string
+  tagFilter?: { tag: string; value: string }
+}
+
 /**
  * #stateModel LinearPileupDisplay
  * extends `BaseLinearDisplay`
@@ -99,6 +106,7 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
          * #property
          */
         mismatchAlpha: types.maybe(types.boolean),
+
         /**
          * #property
          */
@@ -245,7 +253,7 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
 
                 if (
                   !view.initialized ||
-                  !self.estimatedStatsReady ||
+                  !self.featureDensityStatsReady ||
                   self.regionTooLarge
                 ) {
                   return
@@ -331,15 +339,13 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
                       layoutId: view.id,
                       rendererType: 'PileupRenderer',
                     },
-                  )) as { feature: unknown }
+                  )) as { feature: SimpleFeatureSerialized }
 
                   // check featureIdUnderMouse is still the same as the
                   // feature.id that was returned e.g. that the user hasn't
                   // moused over to a new position during the async operation
                   // above
-                  // @ts-expect-error
                   if (self.featureIdUnderMouse === feature.uniqueId) {
-                    // @ts-expect-error
                     self.setFeatureUnderMouse(new SimpleFeature(feature))
                   }
                 }
@@ -403,8 +409,8 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
       /**
        * #action
        */
-      setConfig(configuration: AnyConfigurationModel) {
-        self.configuration = configuration
+      setConfig(conf: AnyConfigurationModel) {
+        self.configuration = conf
       },
 
       /**
@@ -431,12 +437,7 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
         }
         self.ready = false
       },
-      setFilterBy(filter: {
-        flagInclude: number
-        flagExclude: number
-        readName?: string
-        tagFilter?: { tag: string; value: string }
-      }) {
+      setFilterBy(filter: Filter) {
         self.filterBy = cast(filter)
       },
     }))
@@ -456,49 +457,51 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
     })
 
     .views(self => ({
-      /**
-       * #getter
-       */
-      get maxHeight() {
-        const conf = getConf(self, ['renderers', self.rendererTypeName]) || {}
-        return self.trackMaxHeight !== undefined
-          ? self.trackMaxHeight
-          : conf.maxHeight
-      },
-
       /**
        * #getter
        */
       get rendererConfig() {
-        const configBlob =
-          getConf(self, ['renderers', self.rendererTypeName]) || {}
+        const {
+          featureHeight,
+          noSpacing,
+          trackMaxHeight,
+          mismatchAlpha,
+          rendererTypeName,
+        } = self
+        const configBlob = getConf(self, ['renderers', rendererTypeName]) || {}
         return self.rendererType.configSchema.create(
           {
             ...configBlob,
-            height: self.featureHeight,
-            noSpacing: self.noSpacing,
-            maxHeight: this.maxHeight,
-            mismatchAlpha: self.mismatchAlpha,
+            ...(featureHeight !== undefined ? { height: featureHeight } : {}),
+            ...(noSpacing !== undefined ? { noSpacing } : {}),
+            ...(mismatchAlpha !== undefined ? { mismatchAlpha } : {}),
+            ...(trackMaxHeight !== undefined
+              ? { maxHeight: trackMaxHeight }
+              : {}),
           },
           getEnv(self),
         )
       },
+    }))
+    .views(self => ({
+      /**
+       * #getter
+       */
+      get maxHeight() {
+        return readConfObject(self.rendererConfig, 'maxHeight')
+      },
 
       /**
        * #getter
        */
       get featureHeightSetting() {
-        return (
-          self.featureHeight || readConfObject(this.rendererConfig, 'height')
-        )
+        return readConfObject(self.rendererConfig, 'height')
       },
       /**
        * #getter
        */
       get mismatchAlphaSetting() {
-        return self.mismatchAlpha !== undefined
-          ? self.mismatchAlpha
-          : readConfObject(this.rendererConfig, 'mismatchAlpha')
+        return readConfObject(self.rendererConfig, 'mismatchAlpha')
       },
       /**
        * #getter
@@ -614,10 +617,9 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
                       layoutId: getContainingView(self).id,
                       rendererType: 'PileupRenderer',
                     },
-                  )) as { feature: unknown }
+                  )) as { feature: SimpleFeatureSerialized | undefined }
 
                   if (feature) {
-                    // @ts-expect-error
                     self.selectFeature(new SimpleFeature(feature))
                   }
                 }

package/src/LinearReadArcsDisplay/drawFeats.ts

@@ -94,8 +94,8 @@ export default async function drawFeats(
 
     const p1 = f1 ? k1.start : k1.end
     const p2 = hasPaired ? (f2 ? k2.start : k2.end) : f2 ? k2.end : k2.start
-    const ra1 = assembly.getCanonicalRefName(k1.refName)
-    const ra2 = assembly.getCanonicalRefName(k2.refName)
+    const ra1 = assembly.getCanonicalRefName(k1.refName) || k1.refName
+    const ra2 = assembly.getCanonicalRefName(k2.refName) || k2.refName
     const r1 = view.bpToPx({ refName: ra1, coord: p1 })
     const r2 = view.bpToPx({ refName: ra2, coord: p2 })
 

package/src/LinearReadCloudDisplay/drawFeats.ts

@@ -1,4 +1,4 @@
-import { getConf } from '@jbrowse/core/configuration'
+import { AnyConfigurationModel, getConf } from '@jbrowse/core/configuration'
 import { getContainingView, getSession } from '@jbrowse/core/util'
 
 import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
@@ -53,6 +53,7 @@ export default async function drawFeats(
     colorBy?: { type: string }
     height: number
     chainData?: ChainData
+    configuration: AnyConfigurationModel
   },
   ctx: CanvasRenderingContext2D,
 ) {
@@ -82,8 +83,8 @@ export default async function drawFeats(
     if (chain[0].flags & 1 && chain.length > 1) {
       const v0 = chain[0]
       const v1 = chain[1]
-      const ra1 = asm.getCanonicalRefName(v0.refName)
-      const ra2 = asm.getCanonicalRefName(v1.refName)
+      const ra1 = asm.getCanonicalRefName(v0.refName) || v0.refName
+      const ra2 = asm.getCanonicalRefName(v1.refName) || v1.refName
       const r1s = view.bpToPx({ refName: ra1, coord: v0.start })
       const r1e = view.bpToPx({ refName: ra1, coord: v0.end })
       const r2s = view.bpToPx({ refName: ra2, coord: v1.start })
@@ -118,8 +119,8 @@ export default async function drawFeats(
       for (let i = 1; i < chain.length; i++) {
         const v0 = chain[i - 1]
         const v1 = chain[i]
-        const ra1 = asm.getCanonicalRefName(v0.refName)
-        const ra2 = asm.getCanonicalRefName(v1.refName)
+        const ra1 = asm.getCanonicalRefName(v0.refName) || v0.refName
+        const ra2 = asm.getCanonicalRefName(v1.refName) || v1.refName
         const r1s = view.bpToPx({ refName: ra1, coord: v0.start })
         const r1e = view.bpToPx({ refName: ra1, coord: v0.end })
         const r2s = view.bpToPx({ refName: ra2, coord: v1.start })

package/src/LinearSNPCoverageDisplay/models/model.ts

@@ -218,7 +218,7 @@ function stateModelFactory(
 
                 if (
                   !view.initialized ||
-                  !self.estimatedStatsReady ||
+                  !self.featureDensityStatsReady ||
                   self.regionTooLarge
                 ) {
                   return

package/src/PileupRenderer/PileupLayoutSession.ts

@@ -1,6 +1,6 @@
 import deepEqual from 'fast-deep-equal'
 import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType'
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration'
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'
 import GranularRectLayout from '@jbrowse/core/util/layouts/GranularRectLayout'
 import MultiLayout from '@jbrowse/core/util/layouts/MultiLayout'

package/src/PileupRenderer/PileupRenderer.ts

@@ -172,7 +172,7 @@ export default class PileupRenderer extends BoxRendererType {
     // Expand the start and end of feature when softclipping enabled
     if (showSoftClip) {
       const mismatches = feature.get('mismatches') as Mismatch[] | undefined
-      const seq = feature.get('seq') as string
+      const seq = feature.get('seq') as string | undefined
       if (seq && mismatches) {
         for (let i = 0; i < mismatches.length; i += 1) {
           const { type, start, cliplen = 0 } = mismatches[i]
@@ -310,13 +310,16 @@ export default class PileupRenderer extends BoxRendererType {
   }) {
     const heightLim = charHeight - 2
     const { feature, topPx, heightPx } = feat
-    const seq = feature.get('seq') as string
+    const seq = feature.get('seq') as string | undefined
     const cigarOps = parseCigar(feature.get('CIGAR'))
     const w = 1 / bpPerPx
     const start = feature.get('start')
     let soffset = 0 // sequence offset
     let roffset = 0 // reference offset
 
+    if (!seq) {
+      return
+    }
     for (let i = 0; i < cigarOps.length; i += 2) {
       const len = +cigarOps[i]
       const op = cigarOps[i + 1]
@@ -451,9 +454,12 @@ export default class PileupRenderer extends BoxRendererType {
 
     const cigar = feature.get('CIGAR')
     const start = feature.get('start')
-    const seq = feature.get('seq')
+    const seq = feature.get('seq') as string | undefined
     const strand = feature.get('strand')
     const cigarOps = parseCigar(cigar)
+    if (!seq) {
+      return
+    }
 
     const modifications = getModificationPositions(mm, seq, strand)
 
@@ -521,10 +527,14 @@ export default class PileupRenderer extends BoxRendererType {
     const cigar = feature.get('CIGAR')
     const fstart = feature.get('start')
     const fend = feature.get('end')
-    const seq = feature.get('seq')
+    const seq = feature.get('seq') as string | undefined
     const strand = feature.get('strand')
     const cigarOps = parseCigar(cigar)
 
+    if (!seq) {
+      return
+    }
+
     const methBins = new Array(region.end - region.start).fill(0)
     const modifications = getModificationPositions(mm, seq, strand)
     for (let i = 0; i < modifications.length; i++) {
@@ -1035,7 +1045,7 @@ export default class PileupRenderer extends BoxRendererType {
     const [region] = regions
     const minFeatWidth = readConfObject(config, 'minSubfeatureWidth')
     const mismatches = feature.get('mismatches') as Mismatch[] | undefined
-    const seq = feature.get('seq')
+    const seq = feature.get('seq') as string | undefined
     const { charWidth, charHeight } = this.getCharWidthHeight()
     const { bases } = theme.palette
     const colorForBase: { [key: string]: string } = {

package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts

@@ -94,9 +94,12 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
     }, opts.signal)
   }
 
-  async estimateRegionsStats(regions: Region[], opts?: BaseOptions) {
+  async getMultiRegionFeatureDensityStats(
+    regions: Region[],
+    opts?: BaseOptions,
+  ) {
     const { subadapter } = await this.configure()
-    return subadapter.estimateRegionsStats(regions, opts)
+    return subadapter.getMultiRegionFeatureDensityStats(regions, opts)
   }
 
   async getRefNames(opts: BaseOptions = {}) {

package/src/SNPCoverageAdapter/generateCoverageBins.ts

@@ -109,29 +109,30 @@ export default async function generateCoverageBins(
     }
 
     if (colorBy?.type === 'modifications') {
-      const seq = feature.get('seq') as string
+      const seq = feature.get('seq') as string | undefined
       const mm = (getTagAlt(feature, 'MM', 'Mm') as string) || ''
       const ops = parseCigar(feature.get('CIGAR'))
       const fend = feature.get('end')
-
-      getModificationPositions(mm, seq, fstrand).forEach(
-        ({ type, positions }) => {
-          const mod = `mod_${type}`
-          for (const pos of getNextRefPos(ops, positions)) {
-            const epos = pos + fstart - region.start
-            if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
-              const bin = bins[epos]
-              if (bin) {
-                inc(bin, fstrand, 'cov', mod)
-              } else {
-                console.warn(
-                  'Undefined position in modifications snpcoverage encountered',
-                )
+      if (seq) {
+        getModificationPositions(mm, seq, fstrand).forEach(
+          ({ type, positions }) => {
+            const mod = `mod_${type}`
+            for (const pos of getNextRefPos(ops, positions)) {
+              const epos = pos + fstart - region.start
+              if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
+                const bin = bins[epos]
+                if (bin) {
+                  inc(bin, fstrand, 'cov', mod)
+                } else {
+                  console.warn(
+                    'Undefined position in modifications snpcoverage encountered',
+                  )
+                }
               }
             }
-          }
-        },
-      )
+          },
+        )
+      }
     }
 
     // methylation based coloring takes into account both reference
@@ -142,49 +143,51 @@ export default async function generateCoverageBins(
           'no region sequence detected, need sequenceAdapter configuration',
         )
       }
-      const seq = feature.get('seq')
+      const seq = feature.get('seq') as string | undefined
       const mm = getTagAlt(feature, 'MM', 'Mm') || ''
       const methBins = new Array(region.end - region.start).fill(0)
       const ops = parseCigar(feature.get('CIGAR'))
 
-      getModificationPositions(mm, seq, fstrand).forEach(
-        ({ type, positions }) => {
-          // we are processing methylation
-          if (type === 'm') {
-            for (const pos of getNextRefPos(ops, positions)) {
-              const epos = pos + fstart - region.start
-              if (epos >= 0 && epos < methBins.length) {
-                methBins[epos] = 1
+      if (seq) {
+        getModificationPositions(mm, seq, fstrand).forEach(
+          ({ type, positions }) => {
+            // we are processing methylation
+            if (type === 'm') {
+              for (const pos of getNextRefPos(ops, positions)) {
+                const epos = pos + fstart - region.start
+                if (epos >= 0 && epos < methBins.length) {
+                  methBins[epos] = 1
+                }
               }
             }
-          }
-        },
-      )
-
-      for (let j = fstart; j < fend; j++) {
-        const i = j - region.start
-        if (i >= 0 && i < bins.length - 1) {
-          const l1 = regionSeq[i].toLowerCase()
-          const l2 = regionSeq[i + 1].toLowerCase()
-          const bin = bins[i]
-          const bin1 = bins[i + 1]
-
-          // color
-          if (l1 === 'c' && l2 === 'g') {
-            if (methBins[i] || methBins[i + 1]) {
-              inc(bin, fstrand, 'cov', 'meth')
-              inc(bin1, fstrand, 'cov', 'meth')
-              bins[i].ref--
-              bins[i][fstrand]--
-              bins[i + 1].ref--
-              bins[i + 1][fstrand]--
-            } else {
-              inc(bin, fstrand, 'cov', 'unmeth')
-              inc(bin1, fstrand, 'cov', 'unmeth')
-              bins[i].ref--
-              bins[i][fstrand]--
-              bins[i + 1].ref--
-              bins[i + 1][fstrand]--
+          },
+        )
+
+        for (let j = fstart; j < fend; j++) {
+          const i = j - region.start
+          if (i >= 0 && i < bins.length - 1) {
+            const l1 = regionSeq[i].toLowerCase()
+            const l2 = regionSeq[i + 1].toLowerCase()
+            const bin = bins[i]
+            const bin1 = bins[i + 1]
+
+            // color
+            if (l1 === 'c' && l2 === 'g') {
+              if (methBins[i] || methBins[i + 1]) {
+                inc(bin, fstrand, 'cov', 'meth')
+                inc(bin1, fstrand, 'cov', 'meth')
+                bins[i].ref--
+                bins[i][fstrand]--
+                bins[i + 1].ref--
+                bins[i + 1][fstrand]--
+              } else {
+                inc(bin, fstrand, 'cov', 'unmeth')
+                inc(bin1, fstrand, 'cov', 'unmeth')
+                bins[i].ref--
+                bins[i][fstrand]--
+                bins[i + 1].ref--
+                bins[i + 1][fstrand]--
+              }
             }
           }
         }