Use typescript version of @gmod/cram (#3285)

plugins/alignments/package.json

@@ -38,7 +38,7 @@
   },
   "dependencies": {
     "@gmod/bam": "^1.1.15",
-    "@gmod/cram": "^1.6.4",
+    "@gmod/cram": "^1.7.1",
     "@mui/icons-material": "^5.0.1",
     "color": "^3.1.2",
     "copy-to-clipboard": "^3.3.1",

plugins/alignments/src/CramAdapter/CramAdapter.ts

@@ -1,4 +1,4 @@
-import { CraiIndex, IndexedCramFile } from '@gmod/cram'
+import { CraiIndex, IndexedCramFile, CramRecord } from '@gmod/cram'
 import {
   BaseFeatureDataAdapter,
   BaseOptions,
@@ -10,15 +10,10 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import { toArray } from 'rxjs/operators'
 import CramSlightlyLazyFeature from './CramSlightlyLazyFeature'
 
-interface HeaderLine {
-  tag: string
-  value: any // eslint-disable-line @typescript-eslint/no-explicit-any
-  data: HeaderLine[]
-}
 interface Header {
   idToName?: string[]
   nameToId?: Record<string, number>
-  readGroups?: number[]
+  readGroups?: (string | undefined)[]
 }
 
 interface FilterBy {
@@ -33,12 +28,12 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
 
   private setupP?: Promise<{
     samHeader: Header
-    cram: any // eslint-disable-line @typescript-eslint/no-explicit-any
+    cram: IndexedCramFile
     sequenceAdapter: BaseSequenceAdapter
   }>
 
   private configureP?: Promise<{
-    cram: any // eslint-disable-line @typescript-eslint/no-explicit-any
+    cram: IndexedCramFile
     sequenceAdapter: BaseSequenceAdapter
   }>
 
@@ -59,11 +54,10 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     }
     const pm = this.pluginManager
 
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    const cram: any = new IndexedCramFile({
+    const cram = new IndexedCramFile({
       cramFilehandle: openLocation(cramLocation, pm),
       index: new CraiIndex({ filehandle: openLocation(craiLocation, pm) }),
-      seqFetch: this.seqFetch.bind(this),
+      seqFetch: (...args) => this.seqFetch(...args),
       checkSequenceMD5: false,
       fetchSizeLimit: 200_000_000, // just make this a large size to avoid hitting it
     })
@@ -93,16 +87,20 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
 
   async getHeader(opts?: BaseOptions) {
     const { cram } = await this.configure()
-    return cram.cram.getHeaderText(opts)
+    return cram.cram.getHeaderText()
   }
 
-  private async seqFetch(seqId: number, start: number, end: number) {
+  private async seqFetch(
+    seqId: number,
+    start: number,
+    end: number,
+  ): Promise<string> {
     start -= 1 // convert from 1-based closed to interbase
 
     const { sequenceAdapter } = await this.configure()
     const refName = this.refIdToOriginalName(seqId) || this.refIdToName(seqId)
     if (!refName) {
-      return undefined
+      throw new Error('unknown')
     }
 
     const seqChunks = await sequenceAdapter
@@ -145,7 +143,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     const conf = await this.configure()
     statusCallback('Downloading index')
     const { cram } = conf
-    const samHeader: HeaderLine[] = await cram.cram.getSamHeader(opts?.signal)
+    const samHeader = await cram.cram.getSamHeader()
 
     // use the @SQ lines in the header to figure out the
     // mapping between ref ID numbers and names
@@ -237,7 +235,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         this.seqIdToOriginalRefName[refId] = originalRefName
       }
       statusCallback('Downloading alignments')
-      const records = await cram.getRecordsForRange(refId, start, end, opts)
+      const records = await cram.getRecordsForRange(refId, start, end)
       checkAbortSignal(signal)
       const {
         flagInclude = 0,
@@ -246,29 +244,24 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         readName,
       } = filterBy || {}
 
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      let filtered = records.filter((record: any) => {
+      let filtered = records.filter(record => {
         const flags = record.flags
         return (flags & flagInclude) === flagInclude && !(flags & flagExclude)
       })
 
       if (tagFilter) {
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        filtered = filtered.filter((record: any) => {
+        filtered = filtered.filter(record => {
+          // @ts-ignore
           const val = record[tagFilter.tag]
           return val === '*' ? val !== undefined : val === tagFilter.value
         })
       }
 
       if (readName) {
-        filtered = filtered.filter(
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any
-          (record: any) => record.readName === readName,
-        )
+        filtered = filtered.filter(record => record.readName === readName)
       }
 
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      filtered.forEach((record: any) => {
+      filtered.forEach(record => {
         observer.next(this.cramRecordToFeature(record))
       })
       statusCallback('')
@@ -278,7 +271,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
 
   freeResources(/* { region } */): void {}
 
-  cramRecordToFeature(record: unknown) {
+  cramRecordToFeature(record: CramRecord) {
     return new CramSlightlyLazyFeature(record, this)
   }
 
@@ -303,7 +296,9 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
       regions.map(region => {
         const { refName, start, end } = region
         const chrId = this.refNameToId(refName)
-        return cram.index.getEntriesForRange(chrId, start, end)
+        return chrId !== undefined
+          ? cram.index.getEntriesForRange(chrId, start, end)
+          : [{ sliceBytes: 0 }]
       }),
     )
 

plugins/alignments/src/CramAdapter/CramSlightlyLazyFeature.ts

@@ -3,7 +3,7 @@ import {
   Feature,
   SimpleFeatureSerialized,
 } from '@jbrowse/core/util/simpleFeature'
-
+import { CramRecord } from '@gmod/cram'
 import CramAdapter from './CramAdapter'
 
 export interface Mismatch {
@@ -20,8 +20,8 @@ export interface Mismatch {
 export default class CramSlightlyLazyFeature implements Feature {
   // uses parameter properties to automatically create fields on the class
   // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  constructor(private record: any, private _store: CramAdapter) {}
+
+  constructor(private record: CramRecord, private _store: CramAdapter) {}
 
   _get_name() {
     return this.record.readName
@@ -32,7 +32,7 @@ export default class CramSlightlyLazyFeature implements Feature {
   }
 
   _get_end() {
-    return this.record.alignmentStart + this.record.lengthOnRef - 1
+    return this.record.alignmentStart + (this.record.lengthOnRef ?? 1) - 1
   }
 
   _get_cram_read_features() {
@@ -123,6 +123,9 @@ export default class CramSlightlyLazyFeature implements Feature {
     let cigar = ''
     let op = 'M'
     let oplen = 0
+    if (!this.record._refRegion) {
+      return ''
+    }
 
     // not sure I should access these, but...
     const ref = this.record._refRegion.seq
@@ -280,19 +283,12 @@ export default class CramSlightlyLazyFeature implements Feature {
   }
 
   toJSON(): SimpleFeatureSerialized {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    const tags: Record<string, any> = {}
-    this.tags().forEach((t: string) => {
-      const val = this.get(t)
-      if (val !== undefined) {
-        tags[t] = val
-      }
-    })
-
     return {
-      ...tags,
-      name: this.get('name'),
-      type: this.get('type'),
+      ...Object.fromEntries(
+        this.tags()
+          .map(t => [t, this.get(t)])
+          .filter(elt => elt[1] !== undefined),
+      ),
       uniqueId: this.id(),
     }
   }

yarn.lock

@@ -1571,22 +1571,21 @@
   dependencies:
     long "^4.0.0"
 
-"@gmod/cram@^1.6.4":
-  version "1.6.4"
-  resolved "https://registry.yarnpkg.com/@gmod/cram/-/cram-1.6.4.tgz#4c585238ba201381f2e794785f6497b0b2c3bd1a"
-  integrity sha512-uj3BOukiQmL9JwJFMN7qqkvhfWMVVYhymrUA6+z6YMg3u107azw9Oxip6UEUHlVtrJhh2jyLDYgpewFLghJZew==
+"@gmod/cram@^1.7.1":
+  version "1.7.1"
+  resolved "https://registry.yarnpkg.com/@gmod/cram/-/cram-1.7.1.tgz#878f31bc5c038ec789fc0513d769fad5b964a806"
+  integrity sha512-RylBdSTLsKrwp9S1ZDa8hrSRYFRfvDHxH12vM4KrxlIRrpvH5uajGENMigqcL+TQhN9etZeZ+pEBi+lbz8kiXQ==
   dependencies:
     "@gmod/binary-parser" "^1.3.5"
     "@jkbonfield/htscodecs" "^0.5.1"
     abortable-promise-cache "^1.2.0"
     buffer-crc32 "^0.2.13"
     bzip2 "^0.1.1"
     cross-fetch "^3.0.0"
-    es6-promisify "^6.0.1"
     long "^4.0.0"
     md5 "^2.2.1"
     pako "^1.0.4"
-    quick-lru "^2.0.0"
+    quick-lru "^4.0.1"
 
 "@gmod/faidx@^1.0.1":
   version "1.0.3"