Bump deps

GMOD · Feb 21, 2024 · b99d169 · b99d169
1 parent ff057f5
commit b99d169
Show file tree

Hide file tree

Showing 6 changed files with 690 additions and 691 deletions.
diff --git a/package.json b/package.json
@@ -51,7 +51,6 @@
     "@testing-library/react": "^14.0.0",
     "@testing-library/user-event": "^14.4.3",
     "@types/base64-js": "^1.2.5",
-    "@types/buffer-crc32": "^0.2.2",
     "@types/cli-progress": "^3.9.2",
     "@types/command-exists": "^1.2.2",
     "@types/cors": "^2.8.13",

diff --git a/plugins/alignments/src/BamAdapter/BamAdapter.ts b/plugins/alignments/src/BamAdapter/BamAdapter.ts
@@ -90,14 +90,13 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         samHeader
           ?.filter(l => l.tag === 'SQ')
           .forEach((sqLine, refId) => {
-            sqLine.data.forEach(item => {
-              if (item.tag === 'SN') {
-                // this is the ref name
-                const refName = item.value
-                nameToId[refName] = refId
-                idToName[refId] = refName
-              }
-            })
+            const SN = sqLine.data.find(item => item.tag === 'SN')
+            if (SN) {
+              // this is the ref name
+              const refName = SN.value
+              nameToId[refName] = refId
+              idToName[refId] = refName
+            }
           })
 
         return { idToName, nameToId }

diff --git a/plugins/alignments/src/CramAdapter/CramAdapter.ts b/plugins/alignments/src/CramAdapter/CramAdapter.ts
@@ -9,6 +9,7 @@ import {
   Region,
   Feature,
   updateStatus,
+  toLocale,
 } from '@jbrowse/core/util'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
@@ -129,13 +130,14 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
       })
       .join('')
 
-    if (sequence.length !== end - start) {
+    const qlen = end - start
+    if (sequence.length !== qlen) {
       throw new Error(
-        `sequence fetch failed: fetching ${refName}:${(
-          start - 1
-        ).toLocaleString()}-${end.toLocaleString()} returned ${sequence.length.toLocaleString()} bases, but should have returned ${(
-          end - start
-        ).toLocaleString()}`,
+        `fetching ${refName}:${toLocale(
+          start - 1,
+        )}-${toLocale(end)} returned ${toLocale(sequence.length)} bases, should have returned ${toLocale(
+          qlen,
+        )}`,
       )
     }
     return sequence
@@ -155,14 +157,12 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
       samHeader
         .filter(l => l.tag === 'SQ')
         .forEach((sqLine, refId) => {
-          sqLine.data.forEach(item => {
-            if (item.tag === 'SN') {
-              // this is the ref name
-              const refName = item.value!
-              nameToId[refName] = refId
-              idToName[refId] = refName
-            }
-          })
+          const SN = sqLine.data.find(item => item.tag === 'SN')
+          if (SN) {
+            const refName = SN.value
+            nameToId[refName] = refId
+            idToName[refId] = refName
+          }
         })
 
       const readGroups = samHeader
@@ -225,7 +225,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     const { refName, start, end, originalRefName } = region
 
     return ObservableCreate<Feature>(async observer => {
-      const { cram } = await this.setup(opts)
+      const { cram, samHeader } = await this.setup(opts)
 
       const refId = this.refNameToId(refName)
       if (refId === undefined) {
@@ -260,7 +260,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
           if (tagFilter) {
             const v =
               tagFilter.tag === 'RG'
-                ? this.samHeader.readGroups?.[record.readGroupId]
+                ? samHeader.readGroups?.[record.readGroupId]
                 : record.tags[tagFilter.tag]
             if (
               !(tagFilter.value === '*'

diff --git a/plugins/legacy-jbrowse/package.json b/plugins/legacy-jbrowse/package.json
@@ -37,7 +37,7 @@
   },
   "dependencies": {
     "@gmod/nclist": "^0.2.1",
-    "buffer-crc32": "^0.2.13",
+    "buffer-crc32": "^1.0.0",
     "generic-filehandle": "^3.0.0",
     "get-value": "^3.0.1",
     "set-value": "^4.0.1"