Merge branch 'develop' into mh/useTriggerFrame

src/utils/GenomeNavigation.ts

@@ -0,0 +1,183 @@
+/**
+ * HG38 intervals from gosling.js 'computeChromSizes' function
+ */
+function computeForAssembly(assembly?: 'hg38') {
+  if (assembly === 'hg38') {
+    return {
+      interval: {
+        chr1: [0, 248956422],
+        chr2: [248956422, 491149951],
+        chr3: [491149951, 689445510],
+        chr4: [689445510, 879660065],
+        chr5: [879660065, 1061198324],
+        chr6: [1061198324, 1232004303],
+        chr7: [1232004303, 1391350276],
+        chr8: [1391350276, 1536488912],
+        chr9: [1536488912, 1674883629],
+        chr10: [1674883629, 1808681051],
+        chr11: [1808681051, 1943767673],
+        chr12: [1943767673, 2077042982],
+        chr13: [2077042982, 2191407310],
+        chr14: [2191407310, 2298451028],
+        chr15: [2298451028, 2400442217],
+        chr16: [2400442217, 2490780562],
+        chr17: [2490780562, 2574038003],
+        chr18: [2574038003, 2654411288],
+        chr19: [2654411288, 2713028904],
+        chr20: [2713028904, 2777473071],
+        chr21: [2777473071, 2824183054],
+        chr22: [2824183054, 2875001522],
+        chrX: [2875001522, 3031042417],
+        chrY: [3031042417, 3088269832],
+      },
+      size: {
+        chr1: 248956422,
+        chr2: 242193529,
+        chr3: 198295559,
+        chr4: 190214555,
+        chr5: 181538259,
+        chr6: 170805979,
+        chr7: 159345973,
+        chr8: 145138636,
+        chr9: 138394717,
+        chr10: 133797422,
+        chr11: 135086622,
+        chr12: 133275309,
+        chr13: 114364328,
+        chr14: 107043718,
+        chr15: 101991189,
+        chr16: 90338345,
+        chr17: 83257441,
+        chr18: 80373285,
+        chr19: 58617616,
+        chr20: 64444167,
+        chr21: 46709983,
+        chr22: 50818468,
+        chrX: 156040895,
+        chrY: 57227415,
+      },
+      total: 3088269832,
+    };
+  }
+
+  throw new Error('Assembly not supported');
+}
+
+export type ChromKey =
+  | 'chr1'
+  | 'chr2'
+  | 'chr3'
+  | 'chr4'
+  | 'chr5'
+  | 'chr6'
+  | 'chr7'
+  | 'chr8'
+  | 'chr9'
+  | 'chr10'
+  | 'chr11'
+  | 'chr12'
+  | 'chr13'
+  | 'chr14'
+  | 'chr15'
+  | 'chr16'
+  | 'chr17'
+  | 'chr18'
+  | 'chr19'
+  | 'chr20'
+  | 'chr21'
+  | 'chr22'
+  | 'chrX'
+  | 'chrY';
+
+/**
+ * Utility class to convert different types of genomic positions.
+ * The data is taken from gosling.js for hg38 and works similar to `computeChromSizes` in [gosling.js](https://github.com/gosling-lang/gosling.js).
+ *
+ * ### Use cases
+ * - Drawing genome axis
+ * - Working with tile fetchers in gosling
+ * - Fetching transcripts from our backend
+ * - ...
+ *
+ * ### Usage
+ *
+ * ```ts
+ * const nav = new GenomeNavigation('hg38');
+ * const absolutePosition = nav.relativeToAbsolutePosition('chr1', 100);
+ * ```
+ */
+export class GenomeNavigation {
+  private chromosomesInOrder = [...Array.from({ length: 22 }, (_, i) => `chr${i + 1}`), 'chrX', 'chrY'] as ChromKey[];
+
+  private chromosomeSizes: Record<string, number> = {};
+
+  private totalSize = 0;
+
+  private averageSize = 0;
+
+  private interval: Record<ChromKey, [number, number]>;
+
+  constructor(assembly: 'hg38' = 'hg38') {
+    const stats = computeForAssembly(assembly);
+
+    this.chromosomeSizes = stats.size;
+    this.totalSize = stats.total;
+
+    this.interval = stats.interval as Record<ChromKey, [number, number]>;
+
+    this.averageSize = this.totalSize / this.chromosomesInOrder.length;
+  }
+
+  getStartOfChromosome(chrom: string) {
+    return this.interval[chrom as ChromKey]![0];
+  }
+
+  getEndOfChromosome(chrom: string) {
+    return this.interval[chrom as ChromKey]![1];
+  }
+
+  getTotalGenomeSize() {
+    return this.totalSize;
+  }
+
+  relativeToAbsolutePosition(chrom: string, pos: number) {
+    return this.interval[chrom as ChromKey]![0] + pos;
+  }
+
+  getFirstRelativePosition() {
+    return {
+      chromosome: this.chromosomesInOrder[0],
+      position: 0,
+    };
+  }
+
+  getLastRelativePosition() {
+    return {
+      chromosome: this.chromosomesInOrder[this.chromosomesInOrder.length - 1],
+      position: this.chromosomeSizes[this.chromosomesInOrder[this.chromosomesInOrder.length - 1]!]! - 1,
+    };
+  }
+
+  absoluteToRelativePosition(pos: number) {
+    if (pos <= 0) {
+      return this.getFirstRelativePosition();
+    }
+    if (pos >= this.totalSize) {
+      return this.getLastRelativePosition();
+    }
+
+    // Replace with binary search for faster lookup
+    for (let i = 0; i < this.chromosomesInOrder.length; i++) {
+      const chromosome = this.chromosomesInOrder[i]!;
+
+      if (this.interval[chromosome]![0] <= pos && pos < this.interval[chromosome]![1]) {
+        return {
+          chromosome,
+          position: pos - this.interval[chromosome]![0],
+        };
+      }
+    }
+
+    throw new Error('Could not find the chromosome');
+  }
+}

src/utils/index.ts

@@ -4,3 +4,4 @@ export * from './initializeLibrary';
 export * from './fromNow';
 export * from './colors';
 export * from './sanitize-filename';
+export * from './GenomeNavigation';