diff --git a/plugins/variants/src/VcfFeature/__snapshots__/index.test.ts.snap b/plugins/variants/src/VcfFeature/__snapshots__/index.test.ts.snap new file mode 100644 index 0000000000..6923e05b04 --- /dev/null +++ b/plugins/variants/src/VcfFeature/__snapshots__/index.test.ts.snap @@ -0,0 +1,29 @@ +// Jest Snapshot v1, https://goo.gl/fbAQLP + +exports[`null ALT 1`] = ` +{ + "ALT": null, + "CHROM": "chr1", + "FILTER": "PASS", + "ID": [ + "rs123", + ], + "INFO": { + "HELLO": [ + "world", + ], + }, + "POS": 100, + "QUAL": 29, + "REF": "G", + "aliases": undefined, + "description": "no alternative alleles", + "end": 100, + "name": "rs123", + "refName": "chr1", + "samples": {}, + "start": 99, + "type": "remark", + "uniqueId": "myuniqueid", +} +`; diff --git a/plugins/variants/src/VcfFeature/index.test.ts b/plugins/variants/src/VcfFeature/index.test.ts index 8be809d7b5..74e1d38e36 100644 --- a/plugins/variants/src/VcfFeature/index.test.ts +++ b/plugins/variants/src/VcfFeature/index.test.ts @@ -142,3 +142,22 @@ test('multiple SNV2', () => { }) expect(f.get('description')).toEqual('insertion G -> AT,<*>') }) + +// see example 1.1 in VCF 4.3 spec, indicates the . in ALT field indicates +// "a site that is called monomorphic reference (i.e. with no alternate alleles" +test('null ALT', () => { + const parser = new VcfParser({ + header: + '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam', + }) + const line = 'chr1\t100\trs123\tG\t.\t29\tPASS\tHELLO=world' + + const variant = parser.parseLine(line) + + const f = new VcfFeature({ + parser, + variant, + id: 'myuniqueid', + }) + expect(f.toJSON()).toMatchSnapshot() +}) diff --git a/plugins/variants/src/VcfFeature/index.ts b/plugins/variants/src/VcfFeature/index.ts index 16865eff91..ebae983302 100644 --- a/plugins/variants/src/VcfFeature/index.ts +++ b/plugins/variants/src/VcfFeature/index.ts @@ -64,7 +64,7 @@ export default class VCFFeature implements Feature { dataFromVariant(variant: { REF: string POS: number - ALT: string[] + ALT?: string[] CHROM: string INFO: any ID?: string[] @@ -72,8 +72,8 @@ export default class VCFFeature implements Feature { const { REF, ALT, POS, CHROM, INFO, ID } = variant const start = POS - 1 const [type, description] = getSOTermAndDescription(REF, ALT, this.parser) - const isTRA = ALT.includes('') - const isSymbolic = ALT.some(f => f.includes('<')) + const isTRA = ALT?.includes('') + const isSymbolic = ALT?.some(f => f.includes('<')) return { refName: CHROM, diff --git a/products/jbrowse-cli/src/commands/text-index.ts b/products/jbrowse-cli/src/commands/text-index.ts index 288968ec87..25bc8b43a0 100644 --- a/products/jbrowse-cli/src/commands/text-index.ts +++ b/products/jbrowse-cli/src/commands/text-index.ts @@ -361,7 +361,7 @@ export default class TextIndex extends JBrowseCommand { await this.indexDriver({ trackConfigs, outLocation: outFlag, - name: trackConfigs.length > 1 ? 'aggregate' : path.basename(file[0]!), + name: trackConfigs.length > 1 ? 'aggregate' : path.basename(file[0]), quiet, attributes: attributes.split(','), typesToExclude: exclude.split(','), diff --git a/yarn.lock b/yarn.lock index 5eec666bab..7ce63e62cb 100644 --- a/yarn.lock +++ b/yarn.lock @@ -139,9 +139,9 @@ tslib "^2.6.2" "@aws-sdk/client-s3@^3.645.0": - version "3.650.0" - resolved "https://registry.yarnpkg.com/@aws-sdk/client-s3/-/client-s3-3.650.0.tgz#9e8c441afa25575f960ca8b9c44b71c586f38f13" - integrity sha512-6ZfkDu2FMOtYPV1ah5vWMqFKNKEqlBQ3/NOVvLGscU1dR0ybbOwwm4ywWofZmz72uOts5NGqe12kzohb/AsGAA== + version "3.651.0" + resolved "https://registry.yarnpkg.com/@aws-sdk/client-s3/-/client-s3-3.651.0.tgz#289c92c7f7c31733503eeb857c6a5f951e0d9335" + integrity sha512-37+kxxjnlOAUCb1aHpoLakW4XRG23HrkX8X3cEjxaFLQxorPUiMvfAYQEQQkYD5yggaG+5aM5GAhxkTUTqA5xw== dependencies: "@aws-crypto/sha1-browser" "5.2.0" "@aws-crypto/sha256-browser" "5.2.0" @@ -152,7 +152,7 @@ "@aws-sdk/credential-provider-node" "3.650.0" "@aws-sdk/middleware-bucket-endpoint" "3.649.0" "@aws-sdk/middleware-expect-continue" "3.649.0" - 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integrity sha512-mHwRk6UdTkGrLwyYq4Via30kiG2he3d3z1ny0DFlkTQVHZPKpNOf0iROfyZOe31mcjSaTt/eHo7LgEQf1GaXvQ== +nx@19.7.3, "nx@>=17.1.2 < 20": + version "19.7.3" + resolved "https://registry.yarnpkg.com/nx/-/nx-19.7.3.tgz#ca76e9b9fcca9a61a1a65179daef1a3914121b0e" + integrity sha512-8F4CzKavSuOFv+uKVwXHc00Px0q40CWAYCW6NC5IgU3AMaJVumyHzgB8Sn+yfkaVgfVnZVqznOsyrbZUWuj/VA== dependencies: "@napi-rs/wasm-runtime" "0.2.4" - "@nrwl/tao" "19.7.2" + "@nrwl/tao" "19.7.3" "@yarnpkg/lockfile" "^1.1.0" "@yarnpkg/parsers" "3.0.0-rc.46" "@zkochan/js-yaml" "0.0.7" @@ -12516,16 +12527,16 @@ nx@19.7.2, "nx@>=17.1.2 < 20": yargs "^17.6.2" yargs-parser "21.1.1" optionalDependencies: - "@nx/nx-darwin-arm64" "19.7.2" - "@nx/nx-darwin-x64" "19.7.2" - "@nx/nx-freebsd-x64" "19.7.2" - "@nx/nx-linux-arm-gnueabihf" "19.7.2" - "@nx/nx-linux-arm64-gnu" "19.7.2" - "@nx/nx-linux-arm64-musl" "19.7.2" - "@nx/nx-linux-x64-gnu" "19.7.2" - "@nx/nx-linux-x64-musl" "19.7.2" - "@nx/nx-win32-arm64-msvc" "19.7.2" - "@nx/nx-win32-x64-msvc" "19.7.2" + "@nx/nx-darwin-arm64" "19.7.3" + "@nx/nx-darwin-x64" "19.7.3" + "@nx/nx-freebsd-x64" "19.7.3" + "@nx/nx-linux-arm-gnueabihf" "19.7.3" + "@nx/nx-linux-arm64-gnu" "19.7.3" + "@nx/nx-linux-arm64-musl" "19.7.3" + "@nx/nx-linux-x64-gnu" "19.7.3" + "@nx/nx-linux-x64-musl" "19.7.3" + "@nx/nx-win32-arm64-msvc" "19.7.3" + "@nx/nx-win32-x64-msvc" "19.7.3" object-assign@^4, object-assign@^4.0.1, object-assign@^4.1.1: version "4.1.1" @@ -12591,9 +12602,9 @@ obuf@^1.0.0, obuf@^1.1.2: integrity sha512-PX1wu0AmAdPqOL1mWhqmlOd8kOIZQwGZw6rh7uby9fTc5lhaOWFLX3I6R1hrF9k3zUY40e6igsLGkDXK92LJNg== oclif@^4.0.0: - 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