Add automatic aliases for chromosome name case differences (e.g. Chr1…

… vs chr1 vs CHR1)
igvteam · Dec 9, 2024 · 5a0d7ad · 5a0d7ad
1 parent 4164945
commit 5a0d7ad
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Showing 5 changed files with 45 additions and 7 deletions.
diff --git a/js/feature/textFeatureSource.js b/js/feature/textFeatureSource.js
@@ -196,7 +196,7 @@ class TextFeatureSource extends BaseFeatureSource {
         // indicating whole chromosome should be read at once.
         if ((!visibilityWindow || visibilityWindow <= 0) && this.config.expandQuery !== false) {
             // Whole chromosome
-            const chromosome = this.genome ? this.genome.getChromosome(queryChr) : undefined
+            const chromosome = this.genome ? this.genome.getChromosome(chr) : undefined
             intervalStart = 0
             intervalEnd = Math.max(chromosome ? chromosome.bpLength : Number.MAX_SAFE_INTEGER, end)
         } else if (visibilityWindow > (end - start) && this.config.expandQuery !== false) {

diff --git a/js/genome/chromAliasBB.js b/js/genome/chromAliasBB.js
@@ -1,4 +1,5 @@
 import BWReader from "../bigwig/bwReader.js"
+import ChromAliasDefaults from "./chromAliasDefaults.js"
 
 /**
  * Chromosome alias source backed by a UCSC bigbed file
@@ -62,6 +63,7 @@ class ChromAliasBB {
         if (!this.aliasRecordCache.has(alias)) {
             const aliasRecord = await this.reader.search(alias)
             if (aliasRecord) {
+                ChromAliasDefaults.addCaseAliases(aliasRecord)
                 for (let key of Object.keys(aliasRecord)) {
                     if ("start" !== key && "end" !== key) {
                         this.aliasRecordCache.set(aliasRecord[key], aliasRecord)

diff --git a/js/genome/chromAliasDefaults.js b/js/genome/chromAliasDefaults.js
@@ -137,12 +137,12 @@ class ChromAliasDefaults {
                 }
             }
 
+
             for (let rec of aliasRecords) {
+                ChromAliasDefaults.addCaseAliases(rec)
                 for (let a of Object.values(rec)) {
                     this.aliasRecordCache.set(a, rec)
                 }
-                this.aliasRecordCache.set(rec.chr.toLowerCase(), rec)
-                this.aliasRecordCache.set(rec.chr.toUpperCase(), rec)
             }
 
         }
@@ -162,6 +162,24 @@ class ChromAliasDefaults {
         return tokens[tokens.length - 1]
     }
 
+    static addCaseAliases(aliasRecord) {
+
+            // Add some aliases for case insensitivy
+            const upper = aliasRecord.chr.toUpperCase()
+            const lower = aliasRecord.chr.toLowerCase()
+            const cap = aliasRecord.chr.charAt(0).toUpperCase() + aliasRecord.chr.slice(1)
+            if(aliasRecord.chr !== upper) {
+                aliasRecord["_uppercase"] = upper
+            }
+            if(aliasRecord.chr !== lower) {
+                aliasRecord["_lowercase"] = lower
+            }
+            if(aliasRecord.chr !== cap) {
+                aliasRecord["_cap"] = cap
+            }
+
+    }
+
 }
 
 export default ChromAliasDefaults
diff --git a/js/genome/chromAliasFile.js b/js/genome/chromAliasFile.js
@@ -9,8 +9,9 @@
  * @param config
  * @returns {Promise<*[]>}
  */
-import {isNumber, buildOptions} from "../util/igvUtils.js"
+import {buildOptions} from "../util/igvUtils.js"
 import {igvxhr, StringUtils} from "../../node_modules/igv-utils/src/index.js"
+import ChromAliasDefaults from "./chromAliasDefaults.js"
 
 class ChromAliasFile {
 
@@ -73,14 +74,16 @@ class ChromAliasFile {
                 }
 
                 const aliasRecord = {chr}
+                ChromAliasDefaults.addCaseAliases(aliasRecord)
                 for (let i = 0; i < tokens.length; i++) {
                     const key = this.headings ? this.headings[i] : i
                     aliasRecord[key] = tokens[i]
-                    this.aliasRecordCache.set(tokens[i], aliasRecord)
                 }
 
-                this.aliasRecordCache.set(chr.toLowerCase(), aliasRecord)
-                this.aliasRecordCache.set(chr.toUpperCase(), aliasRecord)
+                for (let a of Object.values(aliasRecord)) {
+                    this.aliasRecordCache.set(a, aliasRecord)
+                }
+
             }
         }
     }

diff --git a/js/genome/genome.js b/js/genome/genome.js
@@ -190,6 +190,21 @@ class Genome {
             if (!aliasRecord && chr !== chr.toLowerCase()) {
                 aliasRecord = await this.chromAlias.search(chr.toLowerCase())
             }
+            if(aliasRecord) {
+                // Add some aliases for case insensitivy
+                const upper = aliasRecord.chr.toUpperCase()
+                const lower = aliasRecord.chr.toLowerCase()
+                const cap = aliasRecord.chr.charAt(0).toUpperCase() + aliasRecord.chr.slice(1)
+                if(aliasRecord.chr !== upper) {
+                    aliasRecord["_uppercase"] = upper
+                }
+                if(aliasRecord.chr !== lower) {
+                    aliasRecord["_lowercase"] = lower
+                }
+                if(aliasRecord.chr !== cap) {
+                    aliasRecord["_cap"] = cap
+                }
+            }
             this.#aliasRecordCache.set(chr, aliasRecord)  // Set even if undefined to prevent recurrent searches
             return aliasRecord
         }