@jbrowse/plugin-alignments 2.2.2 → 2.3.1

package/src/CramAdapter/__snapshots__/CramAdapter.test.ts.snap

@@ -13,7 +13,6 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
     "refName": "ctgA",
     "score": 37,
     "seq": "TACACTGGTTCGGAGACGGTTCGTGACGAGCGCGCTATATGTCGGCATCTGCGCCGCATGAGCGGCCGCTGACCGGCGGCACGACTAATATAGTGCAAGA",
-    "seq_id": "ctgA",
     "start": 5440,
     "strand": -1,
     "tags": {
@@ -39,7 +38,6 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
     "refName": "ctgA",
     "score": 37,
     "seq": "ACACTGGTTCGGAGACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCGGCCCCTGTCCGGCGGCACGAATAATATAGTGCAAGAA",
-    "seq_id": "ctgA",
     "start": 5441,
     "strand": -1,
     "tags": {
@@ -65,7 +63,6 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
     "refName": "ctgA",
     "score": 37,
     "seq": "CTGGTTCGGAGACGGTTCATGACGACCGCGCTATATGTCGGCATCTGCGTCGCATGAGCGGCCGCTGTCCGGCGGCTCGAATAATATAGTGCAAGAAAAA",
-    "seq_id": "ctgA",
     "start": 5444,
     "strand": 1,
     "tags": {
@@ -91,7 +88,6 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
     "refName": "ctgA",
     "score": 37,
     "seq": "AGACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCGCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACT",
-    "seq_id": "ctgA",
     "start": 5453,
     "strand": 1,
     "tags": {
@@ -117,7 +113,6 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
     "refName": "ctgA",
     "score": 37,
     "seq": "GACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCCGCCGCTGTCCGACGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTA",
-    "seq_id": "ctgA",
     "start": 5454,
     "strand": 1,
     "tags": {
@@ -143,7 +138,6 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
     "refName": "ctgA",
     "score": 37,
     "seq": "TTCATGACGAGCGCGCTATATGACGGCATCTGCGCCGCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTT",
-    "seq_id": "ctgA",
     "start": 5459,
     "strand": -1,
     "tags": {
@@ -169,7 +163,6 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
     "refName": "ctgA",
     "score": 37,
     "seq": "TCATGACGAGCGCGCTATATGTCGGCATCTGCGCCGCATCAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTA",
-    "seq_id": "ctgA",
     "start": 5460,
     "strand": 1,
     "tags": {
@@ -195,7 +188,6 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
     "refName": "ctgA",
     "score": 37,
     "seq": "AGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTATATATGAT",
-    "seq_id": "ctgA",
     "start": 5468,
     "strand": 1,
     "tags": {
@@ -221,7 +213,6 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
     "refName": "ctgA",
     "score": 37,
     "seq": "CCCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCTAAGACTACGGTTATATATGATGGAACGGCCCTCACAGCATTCTCACA",
-    "seq_id": "ctgA",
     "start": 5494,
     "strand": -1,
     "tags": {
@@ -247,7 +238,6 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
     "refName": "ctgA",
     "score": 37,
     "seq": "CATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTATATATGATGGAACGGCCCTCACAGCATTGTAACAGG",
-    "seq_id": "ctgA",
     "start": 5496,
     "strand": 1,
     "tags": {

package/src/CramAdapter/index.ts

@@ -8,6 +8,7 @@ export default (pluginManager: PluginManager) => {
   pluginManager.addAdapterType(() => {
     return new AdapterType({
       name: 'CramAdapter',
+      displayName: 'CRAM adapter',
       configSchema,
       getAdapterClass: () => import('./CramAdapter').then(r => r.default),
     })

package/src/GuessAlignmentsTypes/index.ts

@@ -0,0 +1,79 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import { FileLocation } from '@jbrowse/core/util/types'
+import {
+  makeIndex,
+  makeIndexType,
+  getFileName,
+  AdapterGuesser,
+  TrackTypeGuesser,
+} from '@jbrowse/core/util/tracks'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addToExtensionPoint(
+    'Core-guessAdapterForLocation',
+    (adapterGuesser: AdapterGuesser) => {
+      return (
+        file: FileLocation,
+        index?: FileLocation,
+        adapterHint?: string,
+      ) => {
+        const regexGuess = /\.cram$/i
+        const adapterName = 'CramAdapter'
+        const fileName = getFileName(file)
+        const obj = {
+          type: adapterName,
+          cramLocation: file,
+          craiLocation: index || makeIndex(file, '.crai'),
+        }
+        if (regexGuess.test(fileName) && !adapterHint) {
+          return obj
+        } else if (adapterHint === adapterName) {
+          return obj
+        }
+        return adapterGuesser(file, index, adapterHint)
+      }
+    },
+  )
+
+  pluginManager.addToExtensionPoint(
+    'Core-guessAdapterForLocation',
+    (adapterGuesser: AdapterGuesser) => {
+      return (
+        file: FileLocation,
+        index?: FileLocation,
+        adapterHint?: string,
+      ) => {
+        const regexGuess = /\.bam$/i
+        const adapterName = 'BamAdapter'
+        const fileName = getFileName(file)
+        const indexName = index && getFileName(index)
+
+        const obj = {
+          type: adapterName,
+          bamLocation: file,
+          index: {
+            location: index || makeIndex(file, '.bai'),
+            indexType: makeIndexType(indexName, 'CSI', 'BAI'),
+          },
+        }
+        if (regexGuess.test(fileName) && !adapterHint) {
+          return obj
+        } else if (adapterHint === adapterName) {
+          return obj
+        }
+        return adapterGuesser(file, index, adapterHint)
+      }
+    },
+  )
+  pluginManager.addToExtensionPoint(
+    'Core-guessTrackTypeForLocation',
+    (trackTypeGuesser: TrackTypeGuesser) => {
+      return (adapterName: string) => {
+        if (adapterName === 'BamAdapter' || adapterName === 'CramAdapter') {
+          return 'AlignmentsTrack'
+        }
+        return trackTypeGuesser(adapterName)
+      }
+    },
+  )
+}

package/src/HtsgetBamAdapter/index.ts

@@ -3,19 +3,15 @@ import PluginManager from '@jbrowse/core/PluginManager'
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
 
 export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'HtsgetBamAdapter',
-        adapterMetadata: {
-          category: null,
-          hiddenFromGUI: true,
-          displayName: null,
-          description: null,
-        },
-        configSchema,
-        getAdapterClass: () =>
-          import('./HtsgetBamAdapter').then(r => r.default),
-      }),
-  )
+  pluginManager.addAdapterType(() => {
+    return new AdapterType({
+      name: 'HtsgetBamAdapter',
+      displayName: 'Htsget BAM adapter',
+      adapterMetadata: {
+        hiddenFromGUI: true,
+      },
+      configSchema,
+      getAdapterClass: () => import('./HtsgetBamAdapter').then(r => r.default),
+    })
+  })
 }

package/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx

@@ -16,7 +16,7 @@ const useStyles = makeStyles()(() => ({
 }))
 
 function AlignmentsDisplay({ model }: { model: AlignmentsDisplayModel }) {
-  const { PileupDisplay, SNPCoverageDisplay, showPileup, showCoverage } = model
+  const { PileupDisplay, SNPCoverageDisplay } = model
   const { classes } = useStyles()
   const top = SNPCoverageDisplay.height
   return (
@@ -24,35 +24,27 @@ function AlignmentsDisplay({ model }: { model: AlignmentsDisplayModel }) {
       data-testid={`display-${getConf(model, 'displayId')}`}
       style={{ position: 'relative' }}
     >
-      {showCoverage ? (
-        <>
-          <div data-testid="Blockset-snpcoverage">
-            <SNPCoverageDisplay.RenderingComponent model={SNPCoverageDisplay} />
-          </div>
-          <ResizeHandle
-            onDrag={delta => {
-              SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta)
-              return delta
-            }}
-            className={classes.resizeHandle}
-            style={{
-              top,
-            }}
-          />
-        </>
-      ) : null}
+      <div data-testid="Blockset-snpcoverage">
+        <SNPCoverageDisplay.RenderingComponent model={SNPCoverageDisplay} />
+      </div>
+      <ResizeHandle
+        onDrag={delta => {
+          SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta)
+          return delta
+        }}
+        className={classes.resizeHandle}
+        style={{ top }}
+      />
 
-      {showPileup ? (
-        <div
-          data-testid="Blockset-pileup"
-          style={{
-            position: 'absolute',
-            top: showCoverage ? SNPCoverageDisplay.height : 0,
-          }}
-        >
-          <PileupDisplay.RenderingComponent model={PileupDisplay} />
-        </div>
-      ) : null}
+      <div
+        data-testid="Blockset-pileup"
+        style={{
+          position: 'absolute',
+          top,
+        }}
+      >
+        <PileupDisplay.RenderingComponent model={PileupDisplay} />
+      </div>
     </div>
   )
 }

package/src/LinearAlignmentsDisplay/index.ts

@@ -10,6 +10,7 @@ export default function (pluginManager: PluginManager) {
     const configSchema = configSchemaFactory(pluginManager)
     return new DisplayType({
       name: 'LinearAlignmentsDisplay',
+      displayName: 'Alignments display (combination)',
       configSchema,
       stateModel: modelFactory(pluginManager, configSchema),
       trackType: 'AlignmentsTrack',

package/src/LinearAlignmentsDisplay/models/configSchema.ts

@@ -7,9 +7,7 @@ import PluginManager from '@jbrowse/core/PluginManager'
  * has a "pileup" sub-display, where you can see individual reads and a
  * quantitative "snpcoverage" sub-display track showing SNP frequencies
  */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const configModelFactory = (pm: PluginManager) => {
+export default function configModelFactory(pm: PluginManager) {
   return ConfigurationSchema(
     'LinearAlignmentsDisplay',
     {
@@ -17,6 +15,7 @@ const configModelFactory = (pm: PluginManager) => {
        * #slot
        */
       pileupDisplay: pm.getDisplayType('LinearPileupDisplay').configSchema,
+
       /**
        * #slot
        */
@@ -32,6 +31,3 @@ const configModelFactory = (pm: PluginManager) => {
     },
   )
 }
-
-export type AlignmentsConfigModel = ReturnType<typeof configModelFactory>
-export default configModelFactory