hs1 testing

GMOD · Nov 6, 2024 · 768d1a0 · 768d1a0
1 parent 27e9f71
commit 768d1a0
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Showing 2 changed files with 72 additions and 8 deletions.
diff --git a/plugins/bed/src/util.ts b/plugins/bed/src/util.ts
@@ -19,8 +19,6 @@ export interface TranscriptFeat extends MinimalFeature {
   subfeatures: MinimalFeature[]
 }
 
-const SPECIFIC_LENGTH_OF_REPEAT_MASKER_DESCRIPTION_FIELDS = 15
-
 export function ucscProcessedTranscript(feature: TranscriptFeat) {
   const {
     subfeatures: oldSubfeatures,
@@ -299,8 +297,7 @@ export function isUcscProcessedTranscript({
     thickStart &&
     blockCount &&
     strand !== 0 &&
-    description?.trim().split(' ').length !==
-      SPECIFIC_LENGTH_OF_REPEAT_MASKER_DESCRIPTION_FIELDS
+    !isRepeatMaskerDescriptionField(description)
   )
 }
 
@@ -312,11 +309,16 @@ export function arrayify(f?: string | number[]) {
     : undefined
 }
 
+function isRepeatMaskerDescriptionField(
+  description?: string,
+): description is string {
+  const ret = description?.trim().split(' ')
+  return [0, 1, 2, 3, 5, 6].every(s =>
+    ret?.[s] !== undefined ? !Number.isNaN(+ret[s]) : false,
+  )
+}
 export function makeRepeatTrackDescription(description?: string) {
-  if (
-    description?.trim().split(' ').length ===
-    SPECIFIC_LENGTH_OF_REPEAT_MASKER_DESCRIPTION_FIELDS
-  ) {
+  if (isRepeatMaskerDescriptionField(description)) {
     const [
       bitsw_score,
       percent_div,

diff --git a/test_data/hs1.json b/test_data/hs1.json
@@ -0,0 +1,62 @@
+{
+  "assemblies": [
+    {
+      "name": "hs1",
+      "displayName": "Homo sapiens (hs1/T2T-CHM13v2.0)",
+      "sequence": {
+        "type": "ReferenceSequenceTrack",
+        "trackId": "hs1-reference",
+        "adapter": {
+          "type": "TwoBitAdapter",
+          "twoBitLocation": {
+            "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.2bit",
+            "locationType": "UriLocation"
+          },
+          "chromSizesLocation": {
+            "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.chrom.sizes.txt",
+            "locationType": "UriLocation"
+          }
+        }
+      },
+      "refNameAliases": {
+        "adapter": {
+          "type": "RefNameAliasAdapter",
+          "location": {
+            "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.chromAlias.txt",
+            "locationType": "UriLocation"
+          }
+        }
+      },
+      "cytobands": {
+        "adapter": {
+          "type": "BigBedAdapter",
+          "bigBedLocation": {
+            "uri": "https://hgdownload.soe.ucsc.edu/gbdb/hs1/cytoBandMapped/cytoBandMapped.bb"
+          }
+        }
+      }
+    }
+  ],
+  "tracks": [
+    {
+      "type": "FeatureTrack",
+      "trackId": "RepeatMasker.sorted.bed",
+      "name": "RepeatMasker.sorted.bed",
+      "adapter": {
+        "type": "BedTabixAdapter",
+        "bedGzLocation": {
+          "uri": "RepeatMasker.sorted.bed.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "RepeatMasker.sorted.bed.gz.tbi",
+            "locationType": "UriLocation"
+          },
+          "indexType": "TBI"
+        }
+      },
+      "assemblyNames": ["hs1"]
+    }
+  ]
+}