@sjcrh/proteinpaint-front 2.214.0 → 2.216.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (8) hide show
  1. package/bundles.tgz +0 -0
  2. package/package.json +3 -3
  3. package/public/cards/BCF.json +1 -0
  4. package/public/cards/bedj.json +1 -0
  5. package/public/cards/bigwig.json +1 -0
  6. package/public/cards/index.json +0 -10
  7. package/src/index.js +45 -1
  8. package/public/cards/ase.json +0 -99
package/bundles.tgz CHANGED
Binary file
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@sjcrh/proteinpaint-front",
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- "version": "2.214.0",
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+ "version": "2.216.0",
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  "browser": "src/app.js",
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  "main": "src/index.js",
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  "bin": "init.js",
@@ -14,7 +14,7 @@
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  "test:integration": "echo 'TODO: front integration tests'"
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  },
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  "devDependencies": {
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- "@sjcrh/proteinpaint-client": "2.214.0",
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+ "@sjcrh/proteinpaint-client": "2.216.0",
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  "webpack": "^5.76.0",
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  "webpack-cli": "^4.9.2",
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  "webpack-node-externals": "^3.0.0"
@@ -32,5 +32,5 @@
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  "url": "https://github.com/stjude/proteinpaint",
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  "directory": "front"
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  },
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- "_buildTime": "2026-09-28T20:05:27Z"
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+ "_buildTime": "2026-10-03T02:09:11Z"
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  }
package/public/cards/BCF.json CHANGED
@@ -47,6 +47,7 @@
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  },
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  {
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  "label": "Remote BCF file",
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+ "configFeature": "ALLOW_remotefilefromurl",
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  "download": "https://proteinpaint.stjude.org/ppdemo/hg38/bcf/bcfDemoFiles.tar.gz",
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  "message": "If the index file is not available at the same URL or named differently, please include <code>.indexURL</code> in the BCF object.",
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  "urlparam": "?genome=hg38&gene=p53&mds3bcfurl=remote,https://proteinpaint.stjude.org/ppdemo/hg38/bcf/test.bcf.gz",
package/public/cards/bedj.json CHANGED
@@ -299,6 +299,7 @@
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  },
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  {
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  "label": "Remote File",
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+ "configFeature": "ALLOW_remotefilefromurl",
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  "urlparam": "?block=on&genome=hg19&bedjurl=Remote%20file,https://hgdownload.soe.ucsc.edu/gbdb/hg19/knownGene.bb",
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  "runargs": {
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  "parseurl": true,
package/public/cards/bigwig.json CHANGED
@@ -67,6 +67,7 @@
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  },
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  {
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  "label": "Remote File",
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+ "configFeature": "ALLOW_remotefilefromurl",
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  "urlparam": "?block=on&genome=hg19&bigwigurl=BigWig%20remote%20file,https://hgdownload.soe.ucsc.edu/goldenPath/hg19/phyloP100way/hg19.100way.phyloP100way.bw",
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  "runargs":{
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  "parseurl": true,
package/public/cards/index.json CHANGED
@@ -158,16 +158,6 @@
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  "sandboxJson":"arc",
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  "searchterms": []
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  },
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- {
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- "type": "card",
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- "name": "ASE",
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- "section": "tracks",
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- "ribbon": {"text": "beta"},
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- "description": "Allele-specific expression analysis",
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- "image": "https://proteinpaint.stjude.org/ppdemo/images/ase-square.png",
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- "sandboxJson": "ase",
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- "searchterms": ["Allele-specific gene expression"]
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- },
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  {
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  "type": "card",
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  "name": "Gene Fusion",
package/src/index.js CHANGED
@@ -1 +1,45 @@
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- export { runproteinpaint } from '@sjcrh/proteinpaint-client'
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+ import { runproteinpaint } from '@sjcrh/proteinpaint-client'
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+ export { runproteinpaint }
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+
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+ // this entry is only bundled as the PP server's /bin/proteinpaint.js, and so
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+ // the startup check of this page's client version against the served bundle applies
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+ runproteinpaint.enableBundleCheck?.()
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+ mayRetryChunkLoads()
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+
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+ /*
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+ Chunk filenames have a content hash (see webpack.config.js). A chunk request may fail when:
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+ - a new deployment has replaced the chunks that an already loaded page expects, or
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+ - during a rolling deployment, an updated page requests a new chunk from a host that
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+ still serves the previous version
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+
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+ Retry a failed chunk load, which may reach an updated host in the second case,
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+ then notify the user if it still fails.
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+ */
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+ function mayRetryChunkLoads() {
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+ // __webpack_require__ is replaced by webpack with its runtime, which has
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+ // .e() to load a chunk and .u() to get a chunk's filename
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+ if (typeof __webpack_require__ != 'function' || !__webpack_require__.e || !__webpack_require__.u) return
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+ const ensureChunk = __webpack_require__.e
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+ const getChunkFilename = __webpack_require__.u
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+ const retryDelays = [1000, 3000] // milliseconds
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+ const retries = {} // {chunkId: number of retries}
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+
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+ // a retried chunk URL has a query parameter, so that a failed response is not reused from a cache
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+ __webpack_require__.u = chunkId => getChunkFilename(chunkId) + (retries[chunkId] ? `?retry=${retries[chunkId]}` : '')
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+
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+ __webpack_require__.e = async (chunkId, ...args) => {
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+ for (let i = 0; ; i++) {
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+ try {
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+ return await ensureChunk(chunkId, ...args)
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+ } catch (e) {
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+ if (e?.name != 'ChunkLoadError') throw e
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+ if (i >= retryDelays.length) {
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+ runproteinpaint.onChunkLoadError?.(e)
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+ throw e
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+ }
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+ retries[chunkId] = i + 1
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+ await new Promise(resolve => setTimeout(resolve, retryDelays[i]))
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+ }
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+ }
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+ }
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+ }
package/public/cards/ase.json DELETED
@@ -1,99 +0,0 @@
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- {
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- "ppcalls": [
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- {
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- "download":"https://proteinpaint.stjude.org/ppdemo/hg38/ase/aseDemoData.tar.gz",
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- "runargs": {
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- "parseurl": true,
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- "block": true,
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- "nobox": 1,
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- "noheader": 1,
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- "genome": "hg38",
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- "position": "chr5:1252462-1297568",
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- "nativetracks": "RefGene",
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- "tracks": [{
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- "type": "mdssvcnv",
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- "name": "ASE Demo",
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- "checkvcf": {
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- "file": "proteinpaint_demo/hg38/ase/vcf.gz"
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- },
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- "checkrnabam": {
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- "hetsnp_minbaf": 0.2,
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- "hetsnp_maxbaf": 0.8,
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- "samples": {
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- "sample1": {
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- "file": "proteinpaint_demo/hg38/ase/sample1.bam",
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- "totalreads": 172048689,
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- "pairedend": true
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- },
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- "sample2": {
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- "file": "proteinpaint_demo/hg38/ase/sample2.bam",
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- "totalreads": 151710239,
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- "pairedend": true
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- },
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- "sample3": {
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- "file": "proteinpaint_demo/hg38/ase/sample3.bam",
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- "totalreads": 167864903,
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- "pairedend": true
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- },
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- "sample4": {
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- "file": "proteinpaint_demo/hg38/ase/sample4.bam",
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- "totalreads": 153196442,
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- "pairedend": true
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- },
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- "sample12": {
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- "file": "proteinpaint_demo/hg38/ase/sample12.bam",
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- "totalreads": 155650314,
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- "pairedend": true
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- },
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- "sample5": {
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- "file": "proteinpaint_demo/hg38/ase/sample5.bam",
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- "totalreads": 144649042,
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- "pairedend": true
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- },
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- "sample6": {
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- "file": "proteinpaint_demo/hg38/ase/sample6.bam",
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- "totalreads": 170516947,
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- "pairedend": true
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- },
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- "sample7": {
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- "file": "proteinpaint_demo/hg38/ase/sample7.bam",
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- "totalreads": 167971047,
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- "pairedend": true
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- },
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- "sample8": {
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- "file": "proteinpaint_demo/hg38/ase/sample8.bam",
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- "totalreads": 137990338,
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- "pairedend": true
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- },
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- "sample9": {
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- "file": "proteinpaint_demo/hg38/ase/sample9.bam",
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- "totalreads": 150401722,
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- "pairedend": true
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- },
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- "sample10": {
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- "file": "proteinpaint_demo/hg38/ase/sample10.bam",
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- "totalreads": 131681552,
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- "pairedend": true
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- },
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- "sample11": {
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- "file": "proteinpaint_demo/hg38/ase/sample11.bam",
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- "totalreads": 150240544,
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- "pairedend": true
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- }
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- }
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- }
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- }]
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- },
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- "testSpec": {
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- "timeout": 7000,
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- "expected": { "rect": 5, "line": 10 }
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- }
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- }
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- ],
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- "buttons": [
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- {
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- "name": "Documentation",
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- "link": "https://github.com/stjude/proteinpaint/wiki/Tracks#Track-ASE-single-sample"
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- }
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- ]
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- }