@jbrowse/plugin-bed 2.10.0 → 2.10.2

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Files changed (3) hide show
  1. package/dist/util.js +12 -1
  2. package/esm/util.js +12 -1
  3. package/package.json +2 -2
package/dist/util.js CHANGED
@@ -7,6 +7,7 @@ function ucscProcessedTranscript(feature) {
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  // split the blocks into UTR, CDS, and exons
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  const thickStart = feature.get('thickStart');
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  const thickEnd = feature.get('thickEnd');
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+ const refName = feature.get('refName');
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  if (!thickStart && !thickEnd) {
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  return feature;
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  }
@@ -15,7 +16,6 @@ function ucscProcessedTranscript(feature) {
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  .filter(child => child.get('type') === 'block')
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  .sort((a, b) => a.get('start') - b.get('start'))
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  : [];
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- // eslint-disable-next-line @typescript-eslint/no-explicit-any
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  const newChildren = [];
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  blocks.forEach(block => {
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  const start = block.get('start');
@@ -27,6 +27,7 @@ function ucscProcessedTranscript(feature) {
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  type: `${prime}_prime_UTR`,
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  start,
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  end,
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+ refName,
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  });
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  }
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  else if (thickStart > start && thickStart < end && thickEnd >= end) {
@@ -36,10 +37,12 @@ function ucscProcessedTranscript(feature) {
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  type: `${prime}_prime_UTR`,
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  start,
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  end: thickStart,
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+ refName,
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  }, {
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  type: 'CDS',
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  start: thickStart,
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  end,
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+ refName,
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  });
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  }
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  else if (thickStart <= start && thickEnd >= end) {
@@ -48,6 +51,7 @@ function ucscProcessedTranscript(feature) {
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  type: 'CDS',
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  start,
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  end,
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+ refName,
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  });
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  }
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  else if (thickStart > start && thickStart < end && thickEnd < end) {
@@ -58,14 +62,17 @@ function ucscProcessedTranscript(feature) {
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  type: `${leftPrime}_prime_UTR`,
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  start,
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  end: thickStart,
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+ refName,
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  }, {
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  type: `CDS`,
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  start: thickStart,
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  end: thickEnd,
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+ refName,
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  }, {
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  type: `${rightPrime}_prime_UTR`,
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  start: thickEnd,
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  end,
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+ refName,
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  });
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  }
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  else if (thickStart <= start && thickEnd > start && thickEnd < end) {
@@ -75,10 +82,12 @@ function ucscProcessedTranscript(feature) {
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  type: `CDS`,
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  start,
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  end: thickEnd,
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+ refName,
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  }, {
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  type: `${prime}_prime_UTR`,
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  start: thickEnd,
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  end,
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+ refName,
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  });
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  }
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  else if (thickEnd <= start) {
@@ -88,6 +97,7 @@ function ucscProcessedTranscript(feature) {
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  type: `${prime}_prime_UTR`,
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  start,
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  end,
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+ refName,
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  });
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  }
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  });
@@ -135,6 +145,7 @@ function featureData(line, colRef, colStart, colEnd, scoreColumn, parser, unique
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  uniqueId: `${uniqueId}-${b}`,
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  start: bmin,
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  end: bmax,
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+ refName,
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  type: 'block',
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  });
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  }
package/esm/util.js CHANGED
@@ -4,6 +4,7 @@ export function ucscProcessedTranscript(feature) {
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  // split the blocks into UTR, CDS, and exons
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  const thickStart = feature.get('thickStart');
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  const thickEnd = feature.get('thickEnd');
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+ const refName = feature.get('refName');
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  if (!thickStart && !thickEnd) {
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  return feature;
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  }
@@ -12,7 +13,6 @@ export function ucscProcessedTranscript(feature) {
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  .filter(child => child.get('type') === 'block')
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  .sort((a, b) => a.get('start') - b.get('start'))
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  : [];
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- // eslint-disable-next-line @typescript-eslint/no-explicit-any
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  const newChildren = [];
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  blocks.forEach(block => {
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  const start = block.get('start');
@@ -24,6 +24,7 @@ export function ucscProcessedTranscript(feature) {
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  type: `${prime}_prime_UTR`,
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  start,
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  end,
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+ refName,
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  });
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  }
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  else if (thickStart > start && thickStart < end && thickEnd >= end) {
@@ -33,10 +34,12 @@ export function ucscProcessedTranscript(feature) {
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  type: `${prime}_prime_UTR`,
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  start,
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  end: thickStart,
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+ refName,
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  }, {
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  type: 'CDS',
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  start: thickStart,
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  end,
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+ refName,
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  });
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  }
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  else if (thickStart <= start && thickEnd >= end) {
@@ -45,6 +48,7 @@ export function ucscProcessedTranscript(feature) {
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  type: 'CDS',
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  start,
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  end,
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+ refName,
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  });
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  }
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  else if (thickStart > start && thickStart < end && thickEnd < end) {
@@ -55,14 +59,17 @@ export function ucscProcessedTranscript(feature) {
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  type: `${leftPrime}_prime_UTR`,
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  start,
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  end: thickStart,
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+ refName,
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  }, {
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  type: `CDS`,
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  start: thickStart,
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  end: thickEnd,
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+ refName,
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  }, {
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  type: `${rightPrime}_prime_UTR`,
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  start: thickEnd,
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  end,
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+ refName,
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  });
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  }
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  else if (thickStart <= start && thickEnd > start && thickEnd < end) {
@@ -72,10 +79,12 @@ export function ucscProcessedTranscript(feature) {
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  type: `CDS`,
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  start,
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  end: thickEnd,
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+ refName,
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  }, {
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  type: `${prime}_prime_UTR`,
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  start: thickEnd,
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  end,
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+ refName,
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  });
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  }
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  else if (thickEnd <= start) {
@@ -85,6 +94,7 @@ export function ucscProcessedTranscript(feature) {
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  type: `${prime}_prime_UTR`,
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  start,
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  end,
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+ refName,
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  });
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  }
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  });
@@ -131,6 +141,7 @@ export function featureData(line, colRef, colStart, colEnd, scoreColumn, parser,
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  uniqueId: `${uniqueId}-${b}`,
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  start: bmin,
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  end: bmax,
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+ refName,
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  type: 'block',
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  });
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  }
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-bed",
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- "version": "2.10.0",
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+ "version": "2.10.2",
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  "description": "JBrowse 2 bed adapters, tracks, etc.",
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  "keywords": [
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  "jbrowse",
@@ -55,5 +55,5 @@
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  "distModule": "esm/index.js",
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  "srcModule": "src/index.ts",
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  "module": "esm/index.js",
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- "gitHead": "223d8bfb68fd1bacaf22852639ad5920f1b7f43b"
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+ "gitHead": "7ca3b7db337ebd88853e2d96cdab940ed550c4fb"
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  }