igv 3.5.1 → 3.5.2

package/README.md

@@ -18,19 +18,19 @@ Below are examples and a quickstart guide.  See the [developer documentation](ht
 
 # Examples
  
-***[Alignments](https://igv.org/web/release/3.5.1/examples/cram-vcf.html)***
+***[Alignments](https://igv.org/web/release/3.5.2/examples/cram-vcf.html)***
 
-***[Interactions](https://igv.org/web/release/3.5.1/examples/interact.html)***
+***[Interactions](https://igv.org/web/release/3.5.2/examples/interact.html)***
 
-***[Copy number](https://igv.org/web/release/3.5.1/examples/copyNumber.html)***
+***[Copy number](https://igv.org/web/release/3.5.2/examples/copyNumber.html)***
 
-***[Multiple regions](https://igv.org/web/release/3.5.1/examples/multi-locus.html)***
+***[Multiple regions](https://igv.org/web/release/3.5.2/examples/multi-locus.html)***
 
-***[Mutation Annotation Format (MAF)](https://igv.org/web/release/3.5.1/examples/maf-tcga.html)***
+***[Mutation Annotation Format (MAF)](https://igv.org/web/release/3.5.2/examples/maf-tcga.html)***
 
-***[Variant color options](https://igv.org/web/release/3.5.1/examples/variant-colors.html)***
+***[Variant color options](https://igv.org/web/release/3.5.2/examples/variant-colors.html)***
 
-***[More](https://igv.org/web/release/3.5.1/examples/)***
+***[More](https://igv.org/web/release/3.5.2/examples/)***
 
  
 # Quickstart
@@ -39,18 +39,18 @@ Below are examples and a quickstart guide.  See the [developer documentation](ht
 igv.js consists of a single javascript file with no external dependencies.  
 
 Pre-built files for script include, AMD, or CJS module systems (igv.min.js) and an ES6 module (igv.esm.min.js)
-can be downloaded from [https://cdn.jsdelivr.net/npm/igv@3.5.1/dist/](https://cdn.jsdelivr.net/npm/igv@3.5.1/dist/). 
+can be downloaded from [https://cdn.jsdelivr.net/npm/igv@3.5.2/dist/](https://cdn.jsdelivr.net/npm/igv@3.5.2/dist/). 
 
 To import igv as an ES6 module
 
 ```javascript
-import igv from "https://cdn.jsdelivr.net/npm/igv@3.5.1/dist/igv.esm.min.js"
+import igv from "https://cdn.jsdelivr.net/npm/igv@3.5.2/dist/igv.esm.min.js"
 ``` 
 
 Or as a script include (defines the "igv" global)
 
 ```html
-<script src="https://cdn.jsdelivr.net/npm/igv@3.5.1/dist/igv.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/igv@3.5.2/dist/igv.min.js"></script>
 ```   
  
 Alternatively you can install with npm  

package/dist/igv.esm.js

@@ -27011,14 +27011,14 @@ function getAminoAcidLetterWithExonGap(strand, phase, phaseExtentStart, phaseExt
         if (phase) {
             stringA = sequenceInterval.getSequence(phaseExtentStart, phaseExtentEnd);
 
-            if (undefined === stringA) {
+            if (!stringA) {
                 return undefined
             }
 
             [ss, ee] = [getEonStart(riteExon), getEonStart(riteExon) + (3 - phase)];
             stringB = sequenceInterval.getSequence(ss, ee);
 
-            if (undefined === stringB) {
+            if (!stringB) {
                 return undefined
             }
 
@@ -27030,7 +27030,7 @@ function getAminoAcidLetterWithExonGap(strand, phase, phaseExtentStart, phaseExt
         if (remainder) {
             stringB = sequenceInterval.getSequence(remainder.start, remainder.end);
 
-            if (undefined === stringB) {
+            if (!stringB) {
                 return undefined
             }
 
@@ -27038,7 +27038,7 @@ function getAminoAcidLetterWithExonGap(strand, phase, phaseExtentStart, phaseExt
             const leftEnd = getExonEnd(leftExon);
             stringA = sequenceInterval.getSequence(leftEnd - leftPhase, leftEnd);
 
-            if (undefined === stringA) {
+            if (!stringA) {
                 return undefined
             }
 
@@ -42825,6 +42825,49 @@ class Locus {
         const end = Number.parseInt(se[1].replace(/,/g, ""));
         return new Locus({chr, start, end})
     }
+
+    /**
+     * Return true if the locus string represents a single base, e.g. "chr1:12345" or "chr1:12345-12345"
+     * @param locus
+     * @returns {boolean}
+     */
+    static isSingleBaseLocusString(locus) {
+
+        if (!locus || typeof locus !== 'string') {
+            return false
+        }
+
+        const parts = locus.split(':');
+        if (parts.length <= 1) {
+            return false
+        }
+
+        const range = parts[1].replace(/,/g, '');
+        if (!range) {
+            return false
+        }
+
+        const rangeParts = range.split('-');
+        const startString = rangeParts[0];
+        const start = parseInt(startString, 10);
+
+        if (String(start) !== startString || !Number.isInteger(start)) {
+            return false
+        }
+
+        if (rangeParts.length === 1) {
+            return true
+        }
+
+        const endString = rangeParts[1];
+        const end = parseInt(endString, 10);
+
+        if (String(end) !== endString || !Number.isInteger(end)) {
+            return false
+        }
+
+        return start === end
+    }
 }
 
 /*!
@@ -66980,7 +67023,7 @@ function createReferenceFrameList(loci, genome, browserFlanking, minimumBases, v
     })
 }
 
-const _version = "3.5.1";
+const _version = "3.5.2";
 function version() {
     return _version
 }
@@ -74235,6 +74278,12 @@ class Browser {
 
         await this.loadTrackList(nonLocalTrackConfigurations);
 
+        // If an initial locus is defined and represents a single basedo a "search" here.  This will force micro
+        // adjustments after width of track column(s) is known.  This can be an issue when the center gide is shown
+        // Without this adjustment the single base would be off center by a few pixels.
+        if (session.locus && Locus.isSingleBaseLocusString(session.locus)) {
+            await this.search(session.locus);
+        }
     }
 
     cleanHouseForSession() {