igv 3.7.2 → 3.7.3

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/3.7.2/examples/cram-vcf.html)***
+***[Alignments](https://igv.org/web/release/3.7.3/examples/cram-vcf.html)***
 
-***[Interactions](https://igv.org/web/release/3.7.2/examples/interact.html)***
+***[Interactions](https://igv.org/web/release/3.7.3/examples/interact.html)***
 
-***[Copy number](https://igv.org/web/release/3.7.2/examples/copyNumber.html)***
+***[Copy number](https://igv.org/web/release/3.7.3/examples/copyNumber.html)***
 
-***[Multiple regions](https://igv.org/web/release/3.7.2/examples/multi-locus.html)***
+***[Multiple regions](https://igv.org/web/release/3.7.3/examples/multi-locus.html)***
 
-***[Mutation Annotation Format (MAF)](https://igv.org/web/release/3.7.2/examples/maf-tcga.html)***
+***[Mutation Annotation Format (MAF)](https://igv.org/web/release/3.7.3/examples/maf-tcga.html)***
 
-***[Variant color options](https://igv.org/web/release/3.7.2/examples/variant-colors.html)***
+***[Variant color options](https://igv.org/web/release/3.7.3/examples/variant-colors.html)***
 
-***[More](https://igv.org/web/release/3.7.2/examples/)***
+***[More](https://igv.org/web/release/3.7.3/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@3.7.2/dist/](https://cdn.jsdelivr.net/npm/igv@3.7.2/dist/). 
+can be downloaded from [https://cdn.jsdelivr.net/npm/igv@3.7.3/dist/](https://cdn.jsdelivr.net/npm/igv@3.7.3/dist/). 
 
 To import igv as an ES6 module
 
 ```javascript
-import igv from "https://cdn.jsdelivr.net/npm/igv@3.7.2/dist/igv.esm.min.js"
+import igv from "https://cdn.jsdelivr.net/npm/igv@3.7.3/dist/igv.esm.min.js"
 ``` 
 
 Or as a script include (defines the "igv" global)
 
 ```html
-<script src="https://cdn.jsdelivr.net/npm/igv@3.7.2/dist/igv.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/igv@3.7.3/dist/igv.min.js"></script>
 ```   
  
 Alternatively you can install with npm  

package/dist/igv.esm.js

@@ -14765,13 +14765,12 @@ function stripQuotes$1(value) {
 
 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);
     }
@@ -14786,7 +14785,7 @@ function isIntron(type) {
 }
 
 function isCoding(type) {
-    return cdsTypes.has(type) || codonTypes.has(type)
+    return cdsTypes.has(type)
 }
 
 function isUTR(type) {
@@ -14966,12 +14965,17 @@ class GFFTranscript extends GFFFeature {
         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);
         }
 
@@ -14983,6 +14987,11 @@ class GFFTranscript extends GFFFeature {
         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;
@@ -15003,7 +15012,10 @@ class GFFTranscript extends GFFFeature {
                 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;
                 }
             }
@@ -35760,6 +35772,11 @@ function getAminoAcidLetterWithExonGap(strand, phase, phaseExtentStart, phaseExt
         }
 
         if (remainder) {
+
+            if (!riteExon) {
+                return undefined
+            }
+
             stringA = sequenceInterval.getSequence(remainder.start, remainder.end);
 
             if (!stringA) {
@@ -50533,19 +50550,26 @@ class AlignmentBlock {
 
 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
@@ -76650,7 +76674,7 @@ function createReferenceFrameList(loci, genome, browserFlanking, minimumBases, v
     })
 }
 
-const _version = "3.7.2";
+const _version = "3.7.3";
 function version() {
     return _version
 }