@jbrowse/plugin-alignments 1.4.1 → 1.5.2

package/src/SNPCoverageAdapter/SNPCoverageAdapter.test.ts

@@ -1,269 +0,0 @@
-import { toArray } from 'rxjs/operators'
-import { LocalFile } from 'generic-filehandle'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { SnapshotIn } from 'mobx-state-tree'
-import AdapterF from './index'
-import CramAdapterF from '../CramAdapter'
-import BamAdapterF from '../BamAdapter'
-
-import { SequenceAdapter } from '../CramAdapter/CramTestAdapters'
-
-const pluginManager = new PluginManager()
-const {
-  getAdapterClass: getSNPCoverageAdapter,
-  configSchema,
-} = pluginManager.load(AdapterF)
-const {
-  getAdapterClass: getCramAdapter,
-  configSchema: CramConfigSchema,
-} = pluginManager.load(CramAdapterF)
-const {
-  getAdapterClass: getBamAdapter,
-  configSchema: BamConfigSchema,
-} = pluginManager.load(BamAdapterF)
-
-pluginManager.configure()
-
-async function newSNPCoverageWithBam(
-  bamConf: SnapshotIn<typeof BamConfigSchema>,
-) {
-  const BamAdapter = await getBamAdapter()
-  const SNPCoverageAdapter = await getSNPCoverageAdapter()
-  return new SNPCoverageAdapter(configSchema.create({}), async () => {
-    return {
-      dataAdapter: new BamAdapter(BamConfigSchema.create(bamConf)),
-      sessionIds: new Set(),
-    }
-  })
-}
-
-test('SNP adapter can fetch features from volvox.bam using bam subadapter', async () => {
-  const adapter = await newSNPCoverageWithBam({
-    type: 'BamAdapter',
-    bamLocation: {
-      localPath: require.resolve('../../test_data/volvox-sorted.bam'),
-    },
-    index: {
-      location: {
-        localPath: require.resolve('../../test_data/volvox-sorted.bam.bai'),
-      },
-      indexType: 'BAI',
-    },
-  })
-
-  const features = adapter.getFeatures(
-    {
-      assemblyName: 'volvox',
-      refName: 'ctgA',
-      start: 0,
-      end: 20000,
-    },
-    {
-      bpPerPx: 0.2,
-    },
-  )
-
-  const featuresArray = await features.pipe(toArray()).toPromise()
-  expect(featuresArray[0].get('refName')).toBe('ctgA')
-  expect(featuresArray[0].get('snpinfo')).toBeTruthy()
-
-  const featuresJsonArray = featuresArray.map(f => f.toJSON())
-  expect(featuresJsonArray.length).toEqual(19998)
-  expect(featuresJsonArray.slice(1000, 1010)).toMatchSnapshot()
-
-  expect(await adapter.hasDataForRefName('ctgA')).toBe(true)
-})
-
-test('test usage of BamSlightlyLazyFeature toJSON in a SNP adapter', async () => {
-  const adapter = await newSNPCoverageWithBam({
-    type: 'BamAdapter',
-    bamLocation: {
-      localPath: require.resolve('../../test_data/volvox-sorted.bam'),
-    },
-    index: {
-      location: {
-        localPath: require.resolve('../../test_data/volvox-sorted.bam.bai'),
-      },
-      indexType: 'BAI',
-    },
-  })
-
-  const features = adapter.getFeatures({
-    assemblyName: 'volvox',
-    refName: 'ctgA',
-    start: 0,
-    end: 100,
-  })
-  const featuresArray = await features.pipe(toArray()).toPromise()
-  const f = featuresArray[0].toJSON()
-
-  expect(f.refName).toBe('ctgA')
-  expect(f.start).toBe(2)
-  expect(f.end).toBe(3)
-  expect(f.snpinfo).toBeTruthy()
-})
-
-test('test usage of getMultiRegion stats, SNP adapter can generate a domain from BamFile', async () => {
-  const adapter = await newSNPCoverageWithBam({
-    type: 'BamAdapter',
-    bamLocation: {
-      localPath: require.resolve('../../test_data/volvox-sorted.bam'),
-    },
-    index: {
-      location: {
-        localPath: require.resolve('../../test_data/volvox-sorted.bam.bai'),
-      },
-      indexType: 'BAI',
-    },
-  })
-
-  const stats = await adapter.getMultiRegionStats(
-    [
-      {
-        assemblyName: 'volvox',
-        refName: 'ctgA',
-        start: 0,
-        end: 100,
-      },
-    ],
-    {
-      opts: {
-        signal: {
-          aborted: false,
-          onabort: null,
-        },
-        bpPerPx: 0.2,
-      },
-    },
-  )
-
-  expect(Object.keys(stats).length).toEqual(9)
-  expect(stats.scoreMin).toEqual(1)
-  expect(stats.scoreMax).toEqual(13)
-})
-
-async function newSNPCoverageWithCram(
-  cramConf: SnapshotIn<typeof CramConfigSchema>,
-  sequenceFileName: string,
-) {
-  const CramAdapter = await getCramAdapter()
-  const SNPCoverageAdapter = await getSNPCoverageAdapter()
-  return new SNPCoverageAdapter(configSchema.create({}), async () => {
-    return {
-      dataAdapter: new CramAdapter(
-        CramConfigSchema.create(cramConf),
-        async () => {
-          return {
-            dataAdapter: new SequenceAdapter(new LocalFile(sequenceFileName)),
-            sessionIds: new Set(),
-          }
-        },
-      ),
-      sessionIds: new Set(),
-    }
-  })
-}
-
-test('SNP adapter can fetch features from volvox.cram using cram subadapter', async () => {
-  const adapter = await newSNPCoverageWithCram(
-    {
-      type: 'CramAdapter',
-      cramLocation: {
-        localPath: require.resolve('../../test_data/volvox-sorted.cram'),
-      },
-      craiLocation: {
-        localPath: require.resolve('../../test_data/volvox-sorted.cram.crai'),
-      },
-    },
-    require.resolve('../../test_data/volvox.fa'),
-  )
-
-  const features = adapter.getFeatures(
-    {
-      assemblyName: 'volvox',
-      refName: 'ctgA',
-      start: 0,
-      end: 20000,
-    },
-    {
-      bpPerPx: 0.2,
-    },
-  )
-
-  const featuresArray = await features.pipe(toArray()).toPromise()
-  expect(featuresArray[0].get('refName')).toBe('ctgA')
-  expect(featuresArray[0].get('snpinfo')).toBeTruthy()
-
-  const featuresJsonArray = featuresArray.map(f => f.toJSON())
-  expect(featuresJsonArray.length).toEqual(19998)
-  expect(featuresJsonArray.slice(1000, 1010)).toMatchSnapshot()
-  expect(await adapter.hasDataForRefName('ctgA')).toBe(true)
-})
-
-test('test usage of CramSlightlyLazyFeature toJSON in a SNP adapter', async () => {
-  const adapter = await newSNPCoverageWithCram(
-    {
-      type: 'CramAdapter',
-      cramLocation: {
-        localPath: require.resolve('../../test_data/volvox-sorted.cram'),
-      },
-      craiLocation: {
-        localPath: require.resolve('../../test_data/volvox-sorted.cram.crai'),
-      },
-    },
-    require.resolve('../../test_data/volvox.fa'),
-  )
-
-  const features = adapter.getFeatures({
-    assemblyName: 'volvox',
-    refName: 'ctgA',
-    start: 0,
-    end: 100,
-  })
-  const featuresArray = await features.pipe(toArray()).toPromise()
-  const f = featuresArray[0].toJSON()
-
-  expect(f.refName).toBe('ctgA')
-  expect(f.start).toBe(2)
-  expect(f.end).toBe(3)
-  expect(f.snpinfo).toBeTruthy()
-})
-
-test('test usage of getMultiRegion stats, SNP adapter can generate a domain from CramFile', async () => {
-  const adapter = await newSNPCoverageWithCram(
-    {
-      type: 'CramAdapter',
-      cramLocation: {
-        localPath: require.resolve('../../test_data/volvox-sorted.cram'),
-      },
-      craiLocation: {
-        localPath: require.resolve('../../test_data/volvox-sorted.cram.crai'),
-      },
-    },
-    require.resolve('../../test_data/volvox.fa'),
-  )
-
-  const stats = await adapter.getMultiRegionStats(
-    [
-      {
-        assemblyName: 'volvox',
-        refName: 'ctgA',
-        start: 0,
-        end: 100,
-      },
-    ],
-    {
-      opts: {
-        signal: {
-          aborted: false,
-          onabort: null,
-        },
-        bpPerPx: 0.2,
-      },
-    },
-  )
-
-  expect(Object.keys(stats).length).toEqual(9)
-  expect(stats.scoreMin).toEqual(1)
-  expect(stats.scoreMax).toEqual(13)
-})