diff --git a/README.md b/README.md index 7eddb42a6..b99314fd8 100644 --- a/README.md +++ b/README.md @@ -14,23 +14,23 @@ James T Robinson, Helga Thorvaldsdottir, Douglass Turner, Jill P Mesirov, igv.js implementation of the Integrative Genomics Viewer (IGV), Bioinformatics, Volume 39, Issue 1, January 2023, btac830, https://doi.org/10.1093/bioinformatics/btac830 -Below are examples and a quickstart guide. See the [Wiki](https://github.com/igvteam/igv.js/wiki) for more documentation. +Below are examples and a quickstart guide. See the [developer documentation](https://igv.org/doc/igvjs) for more documentation. # Examples -***[Alignments](https://igv.org/web/release/2.15.13/examples/cram-vcf.html)*** +***[Alignments](https://igv.org/web/release/3.0.0/examples/cram-vcf.html)*** -***[Interactions](https://igv.org/web/release/2.15.13/examples/interact.html)*** +***[Interactions](https://igv.org/web/release/3.0.0/examples/interact.html)*** -***[Copy number](https://igv.org/web/release/2.15.13/examples/copyNumber.html)*** +***[Copy number](https://igv.org/web/release/3.0.0/examples/copyNumber.html)*** -***[Multiple regions](https://igv.org/web/release/2.15.13/examples/multi-locus.html)*** +***[Multiple regions](https://igv.org/web/release/3.0.0/examples/multi-locus.html)*** -***[Mutation Annotation Format (MAF)](https://igv.org/web/release/2.15.13/examples/maf-tcga.html)*** +***[Mutation Annotation Format (MAF)](https://igv.org/web/release/3.0.0/examples/maf-tcga.html)*** -***[Variant color options](https://igv.org/web/release/2.15.13/examples/variant-colors.html)*** +***[Variant color options](https://igv.org/web/release/3.0.0/examples/variant-colors.html)*** -***[More](https://igv.org/web/release/2.15.13/examples/)*** +***[More](https://igv.org/web/release/3.0.0/examples/)*** # Quickstart @@ -39,18 +39,18 @@ Below are examples and a quickstart guide. See the [Wiki](https://github.com/ig 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@2.15.13/dist/](https://cdn.jsdelivr.net/npm/igv@2.15.13/dist/). +can be downloaded from [https://cdn.jsdelivr.net/npm/igv@3.0.0/dist/](https://cdn.jsdelivr.net/npm/igv@3.0.0/dist/). To import igv as an ES6 module ```javascript -import igv from "https://cdn.jsdelivr.net/npm/igv@2.15.13/dist/igv.esm.min.js" +import igv from "https://cdn.jsdelivr.net/npm/igv@3.0.0/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/alignment/basemods/6mA_pacbio.json b/dev/alignment/basemods/6mA_pacbio.json index 395b21348..04c2ef3c1 100644 --- a/dev/alignment/basemods/6mA_pacbio.json +++ b/dev/alignment/basemods/6mA_pacbio.json @@ -8,7 +8,7 @@ "url": "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam", "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam.bai", "height": 400, - "name": "PacBio - 6mA 2 Color", + "name": "5mC and 6mA - 2 color mode", "colorBy": "basemod2", "groupBy": "strand", "baseModificationThreshold": 0 @@ -19,7 +19,7 @@ "url": "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam", "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam.bai", "height": 400, - "name": "PacBio - 6mA", + "name": "5mC and 6mA - mono color mode", "colorBy": "basemod", "groupBy": "strand" } diff --git a/examples/base-modifications.html b/examples/base-modifications.html new file mode 100644 index 000000000..dcd2a65b9 --- /dev/null +++ b/examples/base-modifications.html @@ -0,0 +1,57 @@ + + + + + igv.js + + + + +

Base Modifications

+ +
+ + + + + + diff --git a/js/bam/alignmentContainer.js b/js/bam/alignmentContainer.js index f4b1d67ab..eda6df9c9 100644 --- a/js/bam/alignmentContainer.js +++ b/js/bam/alignmentContainer.js @@ -764,7 +764,6 @@ function getGroupValue(al, groupBy, expectedPairOrientation) { // Add cases for other options as needed case 'base': - // Use a string prefix to enforce grouping rules: // 1: alignments with a base at the position // 2: alignments with a gap at the position // 3: alignment that do not overlap the position (or are on a different chromosome) diff --git a/js/version.js b/js/version.js index 75819c8b0..2b386b445 100644 --- a/js/version.js +++ b/js/version.js @@ -1,4 +1,4 @@ -const _version = "2.16.0" +const _version = "3.0.0" function version() { return _version } diff --git a/package.json b/package.json index 3d6cdfb88..b74830704 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "igv", - "version": "2.16.0", + "version": "3.0.0", "main": "dist/igv.esm.js", "browser": "dist/igv.js", "module": "dist/igv.esm.js",