Misc

GMOD · Nov 18, 2024 · 5c6421b · 5c6421b
1 parent 2d52a06
commit 5c6421b
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Showing 6 changed files with 304 additions and 144 deletions.
diff --git a/plugins/bed/src/BedAdapter/__snapshots__/BedAdapter.test.ts.snap b/plugins/bed/src/BedAdapter/__snapshots__/BedAdapter.test.ts.snap
@@ -129,8 +129,15 @@ exports[`adapter can fetch features bed with autosql 1`] = `
     "Variant_Type": "SNP",
     "alcohol_history": "--",
     "alcohol_intensity": "--",
+    "blockCount": 1,
+    "blockSizes": [
+      1,
+    ],
     "bmi": "--",
     "case_id": "09454ed6-64bc-4a35-af44-7c4344623d45",
+    "chromStarts": [
+      0,
+    ],
     "cigarettes_per_day": "--",
     "days_to_death": "--",
     "dbSNP_RS": "novel",
@@ -160,6 +167,8 @@ exports[`adapter can fetch features bed with autosql 1`] = `
         "uniqueId": "test-ctgA-0-0",
       },
     ],
+    "thickEnd": 1815757,
+    "thickStart": 1815756,
     "type": undefined,
     "uniqueId": "test-ctgA-0",
     "weight": "--",

diff --git a/plugins/bed/src/BedTabixAdapter/__snapshots__/BedTabixAdapter.test.ts.snap b/plugins/bed/src/BedTabixAdapter/__snapshots__/BedTabixAdapter.test.ts.snap
@@ -129,8 +129,15 @@ exports[`adapter can fetch features bed with autosql 1`] = `
     "Variant_Type": "SNP",
     "alcohol_history": "--",
     "alcohol_intensity": "--",
+    "blockCount": 1,
+    "blockSizes": [
+      1,
+    ],
     "bmi": "--",
     "case_id": "09454ed6-64bc-4a35-af44-7c4344623d45",
+    "chromStarts": [
+      0,
+    ],
     "cigarettes_per_day": "--",
     "days_to_death": "--",
     "dbSNP_RS": "novel",
@@ -160,6 +167,8 @@ exports[`adapter can fetch features bed with autosql 1`] = `
         "uniqueId": "test-52986-0",
       },
     ],
+    "thickEnd": 1815757,
+    "thickStart": 1815756,
     "type": undefined,
     "uniqueId": "test-52986",
     "weight": "--",

diff --git a/plugins/bed/src/BigBedAdapter/BigBedAdapter.ts b/plugins/bed/src/BigBedAdapter/BigBedAdapter.ts
@@ -19,8 +19,8 @@ import { firstValueFrom, Observer, toArray } from 'rxjs'
 
 // locals
 import {
-  isUcscProcessedTranscript,
-  ucscProcessedTranscript,
+  isUcscTranscript,
+  generateUcscTranscript,
   makeRepeatTrackDescription,
   makeBlocks,
   arrayify,
@@ -199,14 +199,14 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
       })
 
       if (
-        isUcscProcessedTranscript({
+        isUcscTranscript({
           strand,
           blockCount,
           thickStart,
           description,
         })
       ) {
-        const f = ucscProcessedTranscript({
+        const f = generateUcscTranscript({
           ...rest,
           strand,
           uniqueId,