igv 3.7.2 → 3.7.3

package/dist/igv.js

@@ -14771,13 +14771,12 @@
 
    const transcriptTypes = new Set(['transcript', 'primary_transcript', 'processed_transcript', 'mRNA', 'mrna',
        'lnc_RNA', 'miRNA', 'ncRNA', 'rRNA', 'scRNA', 'snRNA', 'snoRNA', 'tRNA']);
-   const cdsTypes = new Set(['CDS', 'cds']);
-   const codonTypes = new Set(['start_codon', 'stop_codon']);
+   const cdsTypes = new Set(['CDS', 'cds', 'start_codon', 'stop_codon']);
    const utrTypes = new Set(['5UTR', '3UTR', 'UTR', 'five_prime_UTR', 'three_prime_UTR', "3'-UTR", "5'-UTR"]);
    const exonTypes = new Set(['exon', 'coding-exon']);
 
    const transcriptPartTypes = new Set();
-   for (let cltn of [cdsTypes, codonTypes, utrTypes, exonTypes]) {
+   for (let cltn of [cdsTypes, utrTypes, exonTypes]) {
        for (let t of cltn) {
            transcriptPartTypes.add(t);
        }
@@ -14792,7 +14791,7 @@
    }
 
    function isCoding(type) {
-       return cdsTypes.has(type) || codonTypes.has(type)
+       return cdsTypes.has(type)
    }
 
    function isUTR(type) {
@@ -14972,12 +14971,17 @@
            if (exon) {
                exon.cdStart = exon.cdStart ? Math.min(cds.start, exon.cdStart) : cds.start;
                exon.cdEnd = exon.cdEnd ? Math.max(cds.end, exon.cdEnd) : cds.end;
-               exon.readingFrame = cds.readingFrame;
-               // TODO -- merge attributes?
+               if (cds.readingFrame !== undefined) {
+                   if (exon.readingFrame === undefined) {
+                       exon.readingFrame = cds.readingFrame;
+                   } else {
+                       // Keep reading frame of first CDS in direction of transcription
+                       if (this.strand === '+') ; else {
+                           exon.readingFrame = cds.readingFrame;
+                       }
+                   }
+               }
            } else {
-               // cds.cdStart = cds.start
-               // cds.cdEnd = cds.end
-               // exons.push(cds)
                console.error("No exon found spanning " + cds.start + "-" + cds.end);
            }
 
@@ -14989,6 +14993,11 @@
            this.cdEnd = this.cdEnd ? Math.max(cds.end, this.cdEnd) : cds.end;
        }
 
+       addTerminalCodon(codon) {
+           // Treat terminal codons as CDS
+           this.addCDS(codon);
+       }
+
        addUTR(utr) {
 
            let exon;
@@ -15009,7 +15018,10 @@
                    if (utr.end < exon.end) {
                        exon.cdStart = utr.end;
                    }
-                   if (utr.start > exon.start) {
+                   // Do not "backup" the cdEnd based on a UTR record.  A stop_codon might extend cdEnd into the UTR, and we
+                   // don't want to quash that with the UTR. Although stop codons are not translated, visually
+                   // they appear as part exonic coding sequence. This is a long established convention,
+                   if (exon.cdEnd === undefined || utr.start > exon.cdEnd) {
                        exon.cdEnd = utr.start;
                    }
                }
@@ -35766,6 +35778,11 @@
            }
 
            if (remainder) {
+
+               if (!riteExon) {
+                   return undefined
+               }
+
                stringA = sequenceInterval.getSequence(remainder.start, remainder.end);
 
                if (!stringA) {
@@ -50539,19 +50556,26 @@
 
    class BamFilter {
        constructor(options) {
-           if (!options) options = {};
-           this.vendorFailed = options.vendorFailed = false !== options.vendorFailed;
-           this.duplicate = options.duplicate = false !== options.duplicate;
+           options = options || {};
+
+           // Default to true unless explicitly set to false
+           this.vendorFailed = options.vendorFailed !== false;
+
+           // Support both 'duplicate' and 'duplicates' as synonyms
+           const duplicateValue = options.duplicate !== undefined ? options.duplicate : options.duplicates;
+           this.duplicate = duplicateValue !== false;
+
            this.secondary = options.secondary || false;
            this.supplementary = options.supplementary || false;
            this.mq = options.mq || 0;
+
            if (options.readgroups) {
                this.readgroups = new Set(options.readgroups);
            }
        }
 
        pass(alignment) {
-           if(!alignment.isMapped()) return false
+           if (!alignment.isMapped()) return false
            if (this.vendorFailed && alignment.isFailsVendorQualityCheck()) return false
            if (this.duplicate && alignment.isDuplicate()) return false
            if (this.secondary && alignment.isSecondary()) return false
@@ -76656,7 +76680,7 @@ ${indent}columns: ${matrix.columns}
        })
    }
 
-   const _version = "3.7.2";
+   const _version = "3.7.3";
    function version() {
        return _version
    }