Bump version.

Unit test maintenance.

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/3.0.5/examples/cram-vcf.html)***
+***[Alignments](https://igv.org/web/release/3.0.6/examples/cram-vcf.html)***
 
-***[Interactions](https://igv.org/web/release/3.0.5/examples/interact.html)***
+***[Interactions](https://igv.org/web/release/3.0.6/examples/interact.html)***
 
-***[Copy number](https://igv.org/web/release/3.0.5/examples/copyNumber.html)***
+***[Copy number](https://igv.org/web/release/3.0.6/examples/copyNumber.html)***
 
-***[Multiple regions](https://igv.org/web/release/3.0.5/examples/multi-locus.html)***
+***[Multiple regions](https://igv.org/web/release/3.0.6/examples/multi-locus.html)***
 
-***[Mutation Annotation Format (MAF)](https://igv.org/web/release/3.0.5/examples/maf-tcga.html)***
+***[Mutation Annotation Format (MAF)](https://igv.org/web/release/3.0.6/examples/maf-tcga.html)***
 
-***[Variant color options](https://igv.org/web/release/3.0.5/examples/variant-colors.html)***
+***[Variant color options](https://igv.org/web/release/3.0.6/examples/variant-colors.html)***
 
-***[More](https://igv.org/web/release/3.0.5/examples/)***
+***[More](https://igv.org/web/release/3.0.6/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/[email protected].5/dist/](https://cdn.jsdelivr.net/npm/[email protected].5/dist/). 
+can be downloaded from [https://cdn.jsdelivr.net/npm/[email protected].6/dist/](https://cdn.jsdelivr.net/npm/[email protected].6/dist/). 
 
 To import igv as an ES6 module
 
 ```javascript
-import igv from "https://cdn.jsdelivr.net/npm/[email protected].5/dist/igv.esm.min.js"
+import igv from "https://cdn.jsdelivr.net/npm/[email protected].6/dist/igv.esm.min.js"
 ``` 
 
 Or as a script include (defines the "igv" global)
 
 ```html
-<script src="https://cdn.jsdelivr.net/npm/[email protected].5/dist/igv.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/[email protected].6/dist/igv.min.js"></script>
 ```   
 
 Alternatively you can install with npm  

dev/annotation/gff.html

@@ -23,8 +23,8 @@ <h1>gff and gtf files</h1>
             reference: {
                 "id": "hg38",
                 "name": "Human (GRCh38/hg38)",
-                "fastaURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa",
-                "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa.fai",
+                "fastaURL": "https://igv.org/genomes/data/hg38/hg38.fa",
+                "indexURL": "https://igv.org/genomes/data/hg38/hg38.fa.fai",
                 //"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit",
             },
                 locus: "chr8:127,736,541-127,736,692 chr1:155,186,114-155,186,153",

dev/sampleInfo/sampleInfoFileSession.html

@@ -33,17 +33,7 @@
         {
             "version": "2.16.0",
             "showSampleNames": false,
-            "reference": {
-                "id": "hg38",
-                "name": "Human (GRCh38/hg38)",
-                "fastaURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa",
-                "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa.fai",
-                "cytobandURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/hg38/cytoBandIdeo.txt.gz",
-                "aliasURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/hg38/hg38_alias.tab",
-                "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes",
-                "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit",
-                "chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY"
-            },
+            "genome": "hg38",
             "locus": "chr22:36,655,100-36,656,060",
             "roi": [],
             "tracks": [

js/version.js

@@ -1,4 +1,4 @@
-const _version = "3.0.5"
+const _version = "3.0.6"
 function version() {
     return _version
 }

package.json

@@ -1,6 +1,6 @@
 {
   "name": "igv",
-  "version": "3.0.5",
+  "version": "3.0.6",
   "main": "dist/igv.esm.js",
   "browser": "dist/igv.js",
   "module": "dist/igv.esm.js",

test/data/vcf/noheader.vcf

@@ -3,3 +3,4 @@
 chr6	63498622	<a href='https://www.ncbi.nlm.nih.gov/snp/rs1779765' target='_blank'>rs1779765</a>	T	A	.	.	.
 chr6	63498633	<a href='https://www.ncbi.nlm.nih.gov/snp/rs1779766' target='_blank'>rs1779766</a>	G	A	.	.	.
 chr6	63498639	<a href='https://www.ncbi.nlm.nih.gov/snp/rs1779767' target='_blank'>rs1779767</a>	G	A	.	.	.
+chr6	63498644	.	G	GA,<NON_REF>	.	.	.

test/testGenePred.js

@@ -1,16 +1,6 @@
 import "./utils/mockObjects.js"
 import FeatureFileReader from "../js/feature/featureFileReader.js"
-import FeatureSource from "../js/feature/featureSource.js"
 import {assert} from 'chai'
-import Genome from "../js/genome/genome.js"
-import {decodeGenePredExt} from "../js/feature/decode/ucsc.js"
-
-const reference = {
-    "id": "hg38",
-    "name": "Human (GRCh38/hg38)",
-    "fastaURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa",
-    "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa.fai",
-}
 
 
 suite("testGenePredExt", function () {
@@ -20,7 +10,6 @@ suite("testGenePredExt", function () {
 
         this.timeout(200000)
 
-        const genome = await Genome.createGenome(reference)
 
         const config = {
             format: "refgene",