diff --git a/README.md b/README.md
index 57df80e73..ccdd7ae56 100644
--- a/README.md
+++ b/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/igv@3.0.5/dist/](https://cdn.jsdelivr.net/npm/igv@3.0.5/dist/).
+can be downloaded from [https://cdn.jsdelivr.net/npm/igv@3.0.6/dist/](https://cdn.jsdelivr.net/npm/igv@3.0.6/dist/).
To import igv as an ES6 module
```javascript
-import igv from "https://cdn.jsdelivr.net/npm/igv@3.0.5/dist/igv.esm.min.js"
+import igv from "https://cdn.jsdelivr.net/npm/igv@3.0.6/dist/igv.esm.min.js"
```
Or as a script include (defines the "igv" global)
```html
-
+
```
Alternatively you can install with npm
diff --git a/dev/annotation/gff.html b/dev/annotation/gff.html
index 6eff37306..7bbe7f5f1 100644
--- a/dev/annotation/gff.html
+++ b/dev/annotation/gff.html
@@ -23,8 +23,8 @@ gff and gtf files
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",
diff --git a/dev/issues/issue_1643.html b/dev/issues/issue_1643.html
deleted file mode 100644
index 1019f2dbf..000000000
--- a/dev/issues/issue_1643.html
+++ /dev/null
@@ -1,35 +0,0 @@
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/dev/sampleInfo/sampleInfoFileSession.html b/dev/sampleInfo/sampleInfoFileSession.html
index 0dd82eabd..8b4626df6 100644
--- a/dev/sampleInfo/sampleInfoFileSession.html
+++ b/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": [
diff --git a/js/version.js b/js/version.js
index 0c5511e76..61edc53da 100644
--- a/js/version.js
+++ b/js/version.js
@@ -1,4 +1,4 @@
-const _version = "3.0.5"
+const _version = "3.0.6"
function version() {
return _version
}
diff --git a/package.json b/package.json
index f205705c3..5ce36af5a 100644
--- a/package.json
+++ b/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",
diff --git a/test/data/vcf/noheader.vcf b/test/data/vcf/noheader.vcf
index d01ca839a..4781cf246 100644
--- a/test/data/vcf/noheader.vcf
+++ b/test/data/vcf/noheader.vcf
@@ -3,3 +3,4 @@
chr6 63498622 rs1779765 T A . . .
chr6 63498633 rs1779766 G A . . .
chr6 63498639 rs1779767 G A . . .
+chr6 63498644 . G GA, . . .
diff --git a/test/testGenePred.js b/test/testGenePred.js
index baa5d2b9b..b9efd48da 100644
--- a/test/testGenePred.js
+++ b/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",