gosling.js 2.0.0-alpha.8 → 2.0.0-alpha.9

package/dist/{exported-utils-9e651c40.js → exported-utils-bca41fe4.js}

@@ -9911,8 +9911,25 @@ function getChromTotalSize(chromSize) {
   return Object.values(chromSize).reduce((sum, current) => sum + current, 0);
 }
 function parseGenomicPosition(position) {
-  const [chromosome, intervalString] = position.split(":");
-  if (intervalString) {
+  const firstColonIndex = position.indexOf(":");
+  if (firstColonIndex === -1) {
+    return { chromosome: position };
+  }
+  const chromosome = position.substring(0, firstColonIndex);
+  const intervalString = position.substring(firstColonIndex + 1);
+  if (intervalString.includes(":")) {
+    const dashIndex = intervalString.indexOf("-");
+    if (dashIndex !== -1) {
+      const startPosStr = intervalString.substring(0, dashIndex);
+      const endPart = intervalString.substring(dashIndex + 1);
+      const [chromosomeEnd, endPosStr] = endPart.split(":");
+      const start = +startPosStr.replace(/,/g, "");
+      const end = +endPosStr.replace(/,/g, "");
+      if (!Number.isNaN(start) && !Number.isNaN(end)) {
+        return { chromosome, start, chromosomeEnd, end };
+      }
+    }
+  } else {
     const [start, end] = intervalString.split("-").map((s) => +s.replace(/,/g, ""));
     if (!Number.isNaN(start) && !Number.isNaN(end)) {
       return { chromosome, start, end };
@@ -9921,14 +9938,15 @@ function parseGenomicPosition(position) {
   return { chromosome };
 }
 class GenomicPositionHelper {
-  constructor(chromosome, start, end) {
+  constructor(chromosome, start, end, chromosomeEnd) {
     this.chromosome = chromosome;
     this.start = start;
     this.end = end;
+    this.chromosomeEnd = chromosomeEnd;
   }
   static fromString(str) {
     const result = parseGenomicPosition(str);
-    return new GenomicPositionHelper(result.chromosome, result.start, result.end);
+    return new GenomicPositionHelper(result.chromosome, result.start, result.end, result.chromosomeEnd);
   }
   toAbsoluteCoordinates(assembly, padding = 0) {
     const info = computeChromSizes(assembly);
@@ -9942,6 +9960,15 @@ class GenomicPositionHelper {
       [start, end] = [1, size];
     }
     const offset = interval[0];
+    if (this.chromosomeEnd && this.chromosomeEnd !== this.chromosome) {
+      const endSize = info.size[this.chromosomeEnd];
+      const endInterval = info.interval[this.chromosomeEnd];
+      if (endSize === void 0 || endInterval === void 0) {
+        throw new Error(`End chromosome name ${this.chromosomeEnd} is not valid`);
+      }
+      const endOffset = endInterval[0];
+      return [start + offset - padding, end + endOffset + padding];
+    }
     return [start + offset - padding, end + offset + padding];
   }
 }
@@ -10015,4 +10042,4 @@ export {
   commonjsGlobal as y,
   RemoteFile as z
 };
-//# sourceMappingURL=exported-utils-9e651c40.js.map
+//# sourceMappingURL=exported-utils-bca41fe4.js.map