From 0b4a340372134a7f06424fbcb196e470b98dfcf6 Mon Sep 17 00:00:00 2001 From: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Wed, 25 Sep 2024 09:20:32 -0700 Subject: [PATCH] Bump version. Unit test maintenance. --- README.md | 20 ++++++------- dev/annotation/gff.html | 4 +-- dev/issues/issue_1643.html | 35 ----------------------- dev/sampleInfo/sampleInfoFileSession.html | 12 +------- js/version.js | 2 +- package.json | 2 +- test/data/vcf/noheader.vcf | 1 + test/testGenePred.js | 11 ------- 8 files changed, 16 insertions(+), 71 deletions(-) delete mode 100644 dev/issues/issue_1643.html 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",