From 23caaca9873d92916102a2edc53e23580ab34219 Mon Sep 17 00:00:00 2001 From: Colin Date: Tue, 15 Dec 2020 14:34:46 -0500 Subject: [PATCH 1/2] Change --type to --trackType --- products/jbrowse-cli/src/commands/add-track.test.ts | 2 +- products/jbrowse-cli/src/commands/add-track.ts | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/products/jbrowse-cli/src/commands/add-track.test.ts b/products/jbrowse-cli/src/commands/add-track.test.ts index f3f22a64ce..1c0742c7eb 100644 --- a/products/jbrowse-cli/src/commands/add-track.test.ts +++ b/products/jbrowse-cli/src/commands/add-track.test.ts @@ -265,7 +265,7 @@ describe('add-track', () => { 'customTrackId', '--description', 'new description', - '--type', + '--trackType', 'CustomTrackType', '--category', 'newcategory', diff --git a/products/jbrowse-cli/src/commands/add-track.ts b/products/jbrowse-cli/src/commands/add-track.ts index 7a3d3c9a42..907b2b9e25 100644 --- a/products/jbrowse-cli/src/commands/add-track.ts +++ b/products/jbrowse-cli/src/commands/add-track.ts @@ -39,7 +39,7 @@ export default class AddTrack extends JBrowseCommand { '$ jbrowse add-track /path/to/my.bam --load copy', '$ jbrowse add-track /path/to/my.bam --target /path/to/jbrowse2/installation/config.json --load symlink', '$ jbrowse add-track https://mywebsite.com/my.bam', - `$ jbrowse add-track /path/to/my.bam --type AlignmentsTrack --name 'New Track' --load move`, + `$ jbrowse add-track /path/to/my.bam --trackType AlignmentsTrack --name 'New Track' --load move`, `$ jbrowse add-track /path/to/my.bam --trackId AlignmentsTrack1 --load inPlace --overwrite`, `$ jbrowse add-track /path/to/my.bam --config '{"defaultRendering": "density"}'`, ] @@ -53,7 +53,7 @@ export default class AddTrack extends JBrowseCommand { ] static flags = { - type: flags.string({ + trackType: flags.string({ char: 't', description: `Type of track, by default inferred from track file`, }), From f7831442b99d6bd8e5abb961f9dfe4622eee9df9 Mon Sep 17 00:00:00 2001 From: Colin Date: Tue, 15 Dec 2020 14:37:37 -0500 Subject: [PATCH 2/2] Rename type to trackType --- products/jbrowse-cli/src/commands/add-track.ts | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/products/jbrowse-cli/src/commands/add-track.ts b/products/jbrowse-cli/src/commands/add-track.ts index 907b2b9e25..88562b2c5e 100644 --- a/products/jbrowse-cli/src/commands/add-track.ts +++ b/products/jbrowse-cli/src/commands/add-track.ts @@ -143,7 +143,7 @@ export default class AddTrack extends JBrowseCommand { const isDir = (await fsPromises.lstat(output)).isDirectory() this.target = isDir ? `${output}/config.json` : output - let { type, trackId, name, assemblyNames } = runFlags + let { trackType, trackId, name, assemblyNames } = runFlags const configDirectory = path.dirname(this.target) if (!argsTrack) { @@ -208,7 +208,7 @@ export default class AddTrack extends JBrowseCommand { } // set up the track information - type = type || this.guessTrackType(adapter.type) + const type = trackType || this.guessTrackType(adapter.type) trackId = trackId || path.basename(location, path.extname(location)) name = name || trackId assemblyNames = assemblyNames || configContents.assemblies[0].name