igv 3.4.0 → 3.4.1

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/3.3.0/examples/cram-vcf.html)***
+***[Alignments](https://igv.org/web/release/3.4.1/examples/cram-vcf.html)***
 
-***[Interactions](https://igv.org/web/release/3.3.0/examples/interact.html)***
+***[Interactions](https://igv.org/web/release/3.4.1/examples/interact.html)***
 
-***[Copy number](https://igv.org/web/release/3.3.0/examples/copyNumber.html)***
+***[Copy number](https://igv.org/web/release/3.4.1/examples/copyNumber.html)***
 
-***[Multiple regions](https://igv.org/web/release/3.3.0/examples/multi-locus.html)***
+***[Multiple regions](https://igv.org/web/release/3.4.1/examples/multi-locus.html)***
 
-***[Mutation Annotation Format (MAF)](https://igv.org/web/release/3.3.0/examples/maf-tcga.html)***
+***[Mutation Annotation Format (MAF)](https://igv.org/web/release/3.4.1/examples/maf-tcga.html)***
 
-***[Variant color options](https://igv.org/web/release/3.3.0/examples/variant-colors.html)***
+***[Variant color options](https://igv.org/web/release/3.4.1/examples/variant-colors.html)***
 
-***[More](https://igv.org/web/release/3.3.0/examples/)***
+***[More](https://igv.org/web/release/3.4.1/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@3.3.0/dist/](https://cdn.jsdelivr.net/npm/igv@3.3.0/dist/). 
+can be downloaded from [https://cdn.jsdelivr.net/npm/igv@3.4.1/dist/](https://cdn.jsdelivr.net/npm/igv@3.4.1/dist/). 
 
 To import igv as an ES6 module
 
 ```javascript
-import igv from "https://cdn.jsdelivr.net/npm/igv@3.3.0/dist/igv.esm.min.js"
+import igv from "https://cdn.jsdelivr.net/npm/igv@3.4.1/dist/igv.esm.min.js"
 ``` 
 
 Or as a script include (defines the "igv" global)
 
 ```html
-<script src="https://cdn.jsdelivr.net/npm/igv@3.3.0/dist/igv.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/igv@3.4.1/dist/igv.min.js"></script>
 ```   
  
 Alternatively you can install with npm  

package/dist/igv.esm.js

@@ -22342,7 +22342,7 @@ function overlaps(item, chrIdx1, startBase, chrIdx2, endBase) {
 }
 
 function getDecoder(definedFieldCount, fieldCount, autoSql, format) {
-
+//biggenepred
     if ("biginteract" === format || (autoSql && ('chromatinInteract' === autoSql.table || 'interact' === autoSql.table))) {
         return decodeInteract
     } else {
@@ -22389,9 +22389,20 @@ function getDecoder(definedFieldCount, fieldCount, autoSql, format) {
                 const extraStart = definedFieldCount;
                 for (let i = extraStart; i < fieldCount; i++) {
                     if (i < autoSql.fields.length) {
+
                         const name = autoSql.fields[i].name;
-                        const value = tokens[i - 3];
-                        feature[name] = value;
+
+                        if (name === "exonFrames") {
+                            const frameOffsets = tokens[i - 3].replace(/,$/, '').split(',');
+                            for (let i = 0; i < feature.exons.length; i++) {
+                                const exon = feature.exons[i];
+                                const fo = parseInt(frameOffsets[i]);
+                                if (fo != -1) exon.readingFrame = fo;
+                            }
+                        } else {
+                            const value = tokens[i - 3];
+                            feature[name] = value;
+                        }
                     }
                 }
             }
@@ -22437,6 +22448,7 @@ function getDecoder(definedFieldCount, fieldCount, autoSql, format) {
 
         return feature
     }
+
 }
 
 function findUTRs(exons, cdStart, cdEnd) {
@@ -23031,7 +23043,7 @@ class BWReader {
                     return false
                 });
                 if (matching.length > 0) {
-                    return matching.reduce((l, f) => (l.end - l.start) > (f.end - f.start) ? l : f, features[0])
+                    return matching.reduce((l, f) => (l.end - l.start) > (f.end - f.start) ? l : f, matching[0])
                 } else {
                     return undefined
                 }
@@ -26925,7 +26937,7 @@ function renderAminoAcidSequence(ctx, strand, leftExon, exon, riteExon, bpStart,
         let aaLetter;
         if (undefined === aminoAcidLetter) {
 
-            if(sequenceInterval.hasSequence(start, end)) {
+            if (sequenceInterval.hasSequence(start, end)) {
 
                 const sequence = sequenceInterval.getSequence(start, end);
                 if (sequence && 3 === sequence.length) {
@@ -27061,7 +27073,8 @@ function renderFeatureLabel(ctx, feature, featureX, featureX1, featureY, referen
     try {
         ctx.save();
 
-        let name = feature.name;
+        const labelField = this.config.labelField ? this.config.labelField : 'name';
+        let name = feature[labelField];
         if (name === undefined && feature.gene) name = feature.gene.name;
         if (name === undefined) name = feature.id || feature.ID;
         if (!name || name === '.') return
@@ -27094,20 +27107,13 @@ function renderFeatureLabel(ctx, feature, featureX, featureX1, featureY, referen
         if (options.labelAllFeatures || xleft > lastLabelX || selected) {
             options.rowLastLabelX[feature.row] = xright;
 
-            if ('y' === options.axis) {
-                // TODO -- is this ever used?
-                ctx.save();
-                IGVGraphics.labelTransformWithContext(ctx, centerX);
-                IGVGraphics.fillText(ctx, name, centerX, labelY, geneFontStyle, transform);
-                ctx.restore();
-            } else {
-                ctx.clearRect(
-                    centerX - textMetrics.width / 2 - 1,
-                    labelY - textMetrics.actualBoundingBoxAscent - 1,
-                    textMetrics.width + 2,
-                    textMetrics.actualBoundingBoxAscent + textMetrics.actualBoundingBoxDescent + 2);
-                IGVGraphics.fillText(ctx, name, centerX, labelY, geneFontStyle, transform);
-            }
+            ctx.clearRect(
+                centerX - textMetrics.width / 2 - 1,
+                labelY - textMetrics.actualBoundingBoxAscent - 1,
+                textMetrics.width + 2,
+                textMetrics.actualBoundingBoxAscent + textMetrics.actualBoundingBoxDescent + 2);
+            IGVGraphics.fillText(ctx, name, centerX, labelY, geneFontStyle, transform);
+
         }
 
     } finally {
@@ -27521,7 +27527,11 @@ class FeatureTrack extends TrackBase {
         // If drawing amino acids fetch cached sequence interval.  It is not needed if track does not support AA, but
         // costs nothing since only a reference to a cached object is fetched.
         if (bpPerPixel < aminoAcidSequenceRenderThreshold) {
-            options.sequenceInterval = this.browser.genome.getSequenceInterval(referenceFrame.chr, bpStart, bpEnd);
+            // Restrict the range requested to the limits: 1-chromosome.bpLength
+            const chromosome = this.browser.genome.getChromosome(referenceFrame.chr);
+            const chromosomeEnd = chromosome.bpLength;
+            options.sequenceInterval = this.browser.genome.getSequenceInterval(referenceFrame.chr,
+                bpStart > 0 ? bpStart : 0, bpEnd > chromosomeEnd ? chromosomeEnd : bpEnd);
         }
 
 
@@ -28626,7 +28636,7 @@ class SequenceTrack {
             }
 
             items.push({
-                label: 'BLAT read sequence',
+                label: 'BLAT visible sequence',
                 click: async () => {
                     let sequence = await this.browser.genome.getSequence(chr, start, end);
                     if (sequence) {
@@ -31264,7 +31274,6 @@ isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/186/305/GCF_000186305.1
         if (t.hasProperty("searchTrix")) {
             config.trixURL = t.getProperty("searchTrix");
         }
-
         if (t.hasProperty("group")) {
             config._group = t.getProperty("group");
             if (this.groupPriorityMap && this.groupPriorityMap.has(config._group)) {
@@ -31273,6 +31282,12 @@ isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/186/305/GCF_000186305.1
                 this.groupPriorityMap.set(config._group, nextPriority);
             }
         }
+        const labelFields = t.hasProperty("defaultLabelFields") ?
+            t.getProperty("defaultLabelFields") :
+            t.getProperty("labelFields");
+        if (labelFields) {
+            config.labelField = labelFields.split(",")[0];
+        }
 
         return config
     }
@@ -31413,9 +31428,9 @@ async function loadStanzas(url) {
             }
 
 
-            const i = line.indexOf(' ');
-            const key = line.substring(0, i).trim();
-            let value = line.substring(i + 1).trim();
+            const index = line.indexOf(' ');
+            const key = line.substring(0, index).trim();
+            let value = line.substring(index + 1).trim();
 
             if (key === "type") {
                 // The "type" property contains format and sometimes other information. For example, data range
@@ -49377,7 +49392,7 @@ class AlignmentTrack extends TrackBase {
 
                     if (seqstring.length < maxSequenceSize$1) {
                         list.push({
-                            label: 'BLAT read sequence',
+                            label: 'BLAT visible sequence',
                             click: () => {
                                 const sequence = clickedAlignment.isNegativeStrand() ? reverseComplementSequence(seqstring) : seqstring;
                                 const name = `${clickedAlignment.readName} - blat`;
@@ -70318,7 +70333,7 @@ function createReferenceFrameList(loci, genome, browserFlanking, minimumBases, v
     })
 }
 
-const _version = "3.4.0";
+const _version = "3.4.1";
 function version() {
     return _version
 }
@@ -74893,7 +74908,10 @@ class Browser {
 
         const locusFound = await this.search(locus, true);
         if (!locusFound) {
-            throw new Error(`Cannot set initial locus ${locus}`)
+            console.error(`Cannot set initial locus ${locus}`);
+            if(locus !== genome.initialLocus) {
+                await this.search(genome.initialLocus);
+            }
         }
 
         if (genomeChange) {