@sjcrh/proteinpaint-server 2.139.1 → 2.140.0
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.
- package/package.json +1 -1
- package/routes/grin2.js +9 -6
- package/src/app.js +23 -10
package/package.json
CHANGED
package/routes/grin2.js
CHANGED
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@@ -203,20 +203,23 @@ function filterAndConvertSnvIndel(sampleName, entry, options) {
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203
203
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return [sampleName, entry.chr, entry.pos, entry.pos, "mutation"];
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204
204
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}
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205
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function filterAndConvertCnv(sampleName, entry, options) {
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206
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-
if (!options || options.gainThreshold === void 0 || options.lossThreshold === void 0) {
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206
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+
if (!options || options.gainThreshold === void 0 || options.lossThreshold === void 0 || options.maxSegLength === void 0) {
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207
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return null;
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}
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209
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-
const isGain = entry.value >= options.gainThreshold;
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210
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-
const isLoss = entry.value <= options.lossThreshold;
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211
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if (!isGain && !isLoss)
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212
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return null;
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213
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-
const lesionType = isGain ? "gain" : "loss";
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214
209
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if (!Number.isInteger(entry.start)) {
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return null;
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}
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if (!Number.isInteger(entry.stop)) {
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return null;
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}
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215
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+
if (options.maxSegLength > 0 && entry.stop - entry.start > options.maxSegLength) {
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216
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return null;
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217
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}
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218
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+
const isGain = entry.value >= options.gainThreshold;
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219
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+
const isLoss = entry.value <= options.lossThreshold;
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220
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if (!isGain && !isLoss)
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221
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return null;
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222
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const lesionType = isGain ? "gain" : "loss";
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return [sampleName, entry.chr, entry.start, entry.stop, lesionType];
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}
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function filterAndConvertFusion(sampleName, entry, _options) {
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