igv 3.4.0 → 3.4.1

package/dist/igv.js

@@ -22348,7 +22348,7 @@
    }
 
    function getDecoder(definedFieldCount, fieldCount, autoSql, format) {
-
+   //biggenepred
        if ("biginteract" === format || (autoSql && ('chromatinInteract' === autoSql.table || 'interact' === autoSql.table))) {
            return decodeInteract
        } else {
@@ -22395,9 +22395,20 @@
                    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;
+                           }
                        }
                    }
                }
@@ -22443,6 +22454,7 @@
 
            return feature
        }
+
    }
 
    function findUTRs(exons, cdStart, cdEnd) {
@@ -23037,7 +23049,7 @@
                        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
                    }
@@ -26931,7 +26943,7 @@
            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) {
@@ -27067,7 +27079,8 @@
        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
@@ -27100,20 +27113,13 @@
            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 {
@@ -27527,7 +27533,11 @@
            // 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);
            }
 
 
@@ -28632,7 +28642,7 @@
                }
 
                items.push({
-                   label: 'BLAT read sequence',
+                   label: 'BLAT visible sequence',
                    click: async () => {
                        let sequence = await this.browser.genome.getSequence(chr, start, end);
                        if (sequence) {
@@ -31270,7 +31280,6 @@
            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)) {
@@ -31279,6 +31288,12 @@
                    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
        }
@@ -31419,9 +31434,9 @@
                }
 
 
-               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
@@ -49383,7 +49398,7 @@
 
                        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`;
@@ -70324,7 +70339,7 @@ ${indent}columns: ${matrix.columns}
        })
    }
 
-   const _version = "3.4.0";
+   const _version = "3.4.1";
    function version() {
        return _version
    }
@@ -74899,7 +74914,10 @@ ${indent}columns: ${matrix.columns}
 
            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) {