@gmod/bbi 1.0.32 → 1.0.33

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Files changed (8) hide show
  1. package/CHANGELOG.md +7 -0
  2. package/dist/bbi.js +5 -5
  3. package/dist/bigbed.js +1 -1
  4. package/dist/blockView.js +5 -5
  5. package/esm/bbi.js +5 -5
  6. package/esm/bigbed.js +1 -1
  7. package/esm/blockView.js +5 -5
  8. package/package.json +1 -1
package/CHANGELOG.md CHANGED
@@ -1,3 +1,10 @@
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+ ## [1.0.33](https://github.com/GMOD/bbi-js/compare/v1.0.32...v1.0.33) (2022-02-25)
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+
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+
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+
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+ - Use subarray instead of slice since slice is deprecated under node xref
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+ 'https://nodejs.org/api/buffer.html#bufslicestart-end'"
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+
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  ## [1.0.32](https://github.com/GMOD/bbi-js/compare/v1.0.31...v1.0.32) (2022-02-16)
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package/dist/bbi.js CHANGED
@@ -192,14 +192,14 @@ var BBI = /** @class */ (function () {
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  }
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  if (header.asOffset) {
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  header.autoSql = buffer
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- .slice(header.asOffset, buffer.indexOf(0, header.asOffset))
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+ .subarray(header.asOffset, buffer.indexOf(0, header.asOffset))
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  .toString('utf8');
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  }
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  if (header.totalSummaryOffset > requestSize) {
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  return [2 /*return*/, this._getMainHeader(opts, requestSize * 2)];
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  }
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  if (header.totalSummaryOffset) {
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- tail = buffer.slice(header.totalSummaryOffset);
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+ tail = buffer.subarray(header.totalSummaryOffset);
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  header.totalSummary = ret.totalSummaryParser.parse(tail).result;
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  }
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  return [2 /*return*/, __assign(__assign({}, header), { isBigEndian: isBigEndian })];
@@ -259,12 +259,12 @@ var BBI = /** @class */ (function () {
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  if (offset >= data.length) {
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  throw new Error('reading beyond end of buffer');
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  }
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- ret = p.isLeafNode.parse(data.slice(offset));
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+ ret = p.isLeafNode.parse(data.subarray(offset));
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  _a = ret.result, isLeafNode = _a.isLeafNode, cnt = _a.cnt;
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  offset += ret.offset;
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  if (!isLeafNode) return [3 /*break*/, 1];
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  for (n = 0; n < cnt; n += 1) {
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- leafRet = leafNodeParser.parse(data.slice(offset));
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+ leafRet = leafNodeParser.parse(data.subarray(offset));
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  offset += leafRet.offset;
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  _b = leafRet.result, key = _b.key, refId = _b.refId, refSize = _b.refSize;
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  refRec = { name: key, id: refId, length: refSize };
@@ -275,7 +275,7 @@ var BBI = /** @class */ (function () {
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  case 1:
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  nextNodes = [];
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  for (n = 0; n < cnt; n += 1) {
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- nonleafRet = nonleafNodeParser.parse(data.slice(offset));
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+ nonleafRet = nonleafNodeParser.parse(data.subarray(offset));
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  childOffset = nonleafRet.result.childOffset;
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  offset += nonleafRet.offset;
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  childOffset -= chromTreeOffset;
package/dist/bigbed.js CHANGED
@@ -150,7 +150,7 @@ var BigBed = /** @class */ (function (_super) {
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  .int16('field');
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  indices = [];
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  for (i = 0; i < count; i += 1) {
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- indices.push(extParser.parse(buffer.slice(i * blocklen)).result);
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+ indices.push(extParser.parse(buffer.subarray(i * blocklen)).result);
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  }
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  return [2 /*return*/, indices];
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  }
package/dist/blockView.js CHANGED
@@ -215,7 +215,7 @@ var BlockView = /** @class */ (function () {
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  outstanding_1 = 0;
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  cirFobRecur2_1 = function (cirBlockData, offset, level) {
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  try {
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- var data = cirBlockData.slice(offset);
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+ var data = cirBlockData.subarray(offset);
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  var p = _this.leafParser.parse(data).result;
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  if (p.blocksToFetch) {
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  blocksToFetch_1 = blocksToFetch_1.concat(p.blocksToFetch.filter(filterFeats_1).map(function (l) { return ({
@@ -299,7 +299,7 @@ var BlockView = /** @class */ (function () {
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  var features = [];
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  var currOffset = startOffset;
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  while (currOffset < data.byteLength) {
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- var res = this.summaryParser.parse(data.slice(currOffset));
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+ var res = this.summaryParser.parse(data.subarray(currOffset));
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  features.push(res.result);
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  currOffset += res.offset;
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  }
@@ -323,7 +323,7 @@ var BlockView = /** @class */ (function () {
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  var items = [];
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  var currOffset = startOffset;
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  while (currOffset < data.byteLength) {
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- var res = this.bigBedParser.parse(data.slice(currOffset));
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+ var res = this.bigBedParser.parse(data.subarray(currOffset));
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  res.result.uniqueId = "bb-".concat(offset + currOffset);
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  items.push(res.result);
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  currOffset += res.offset;
@@ -333,7 +333,7 @@ var BlockView = /** @class */ (function () {
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  : items;
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  };
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  BlockView.prototype.parseBigWigBlock = function (bytes, startOffset, request) {
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- var data = bytes.slice(startOffset);
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+ var data = bytes.subarray(startOffset);
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  var results = this.bigWigParser.parse(data).result;
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  var items = results.items, itemSpan = results.itemSpan, itemStep = results.itemStep, blockStart = results.blockStart, blockType = results.blockType;
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  if (blockType === BIG_WIG_TYPE_FSTEP) {
@@ -383,7 +383,7 @@ var BlockView = /** @class */ (function () {
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  var blockOffset = block.offset - blockGroup.offset;
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  var resultData = data;
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  if (isCompressed_1) {
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- resultData = (0, unzip_1.unzip)(data.slice(blockOffset));
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+ resultData = (0, unzip_1.unzip)(data.subarray(blockOffset));
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  blockOffset = 0;
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  }
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  (0, util_1.checkAbortSignal)(signal_2);
package/esm/bbi.js CHANGED
@@ -122,14 +122,14 @@ class BBI {
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  }
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  if (header.asOffset) {
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  header.autoSql = buffer
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- .slice(header.asOffset, buffer.indexOf(0, header.asOffset))
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+ .subarray(header.asOffset, buffer.indexOf(0, header.asOffset))
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  .toString('utf8');
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  }
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  if (header.totalSummaryOffset > requestSize) {
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  return this._getMainHeader(opts, requestSize * 2);
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  }
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  if (header.totalSummaryOffset) {
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- const tail = buffer.slice(header.totalSummaryOffset);
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+ const tail = buffer.subarray(header.totalSummaryOffset);
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  header.totalSummary = ret.totalSummaryParser.parse(tail).result;
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  }
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  return { ...header, isBigEndian };
@@ -174,12 +174,12 @@ class BBI {
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  if (offset >= data.length) {
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  throw new Error('reading beyond end of buffer');
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  }
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- const ret = p.isLeafNode.parse(data.slice(offset));
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+ const ret = p.isLeafNode.parse(data.subarray(offset));
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  const { isLeafNode, cnt } = ret.result;
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  offset += ret.offset;
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  if (isLeafNode) {
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  for (let n = 0; n < cnt; n += 1) {
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- const leafRet = leafNodeParser.parse(data.slice(offset));
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+ const leafRet = leafNodeParser.parse(data.subarray(offset));
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  offset += leafRet.offset;
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  const { key, refId, refSize } = leafRet.result;
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  const refRec = { name: key, id: refId, length: refSize };
@@ -191,7 +191,7 @@ class BBI {
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  // parse index node
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  const nextNodes = [];
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  for (let n = 0; n < cnt; n += 1) {
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- const nonleafRet = nonleafNodeParser.parse(data.slice(offset));
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+ const nonleafRet = nonleafNodeParser.parse(data.subarray(offset));
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  let { childOffset } = nonleafRet.result;
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  offset += nonleafRet.offset;
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  childOffset -= chromTreeOffset;
package/esm/bigbed.js CHANGED
@@ -69,7 +69,7 @@ class BigBed extends bbi_1.BBI {
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  .int16('field');
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  const indices = [];
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  for (let i = 0; i < count; i += 1) {
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- indices.push(extParser.parse(buffer.slice(i * blocklen)).result);
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+ indices.push(extParser.parse(buffer.subarray(i * blocklen)).result);
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  }
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  return indices;
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  }
package/esm/blockView.js CHANGED
@@ -150,7 +150,7 @@ class BlockView {
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  let outstanding = 0;
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  const cirFobRecur2 = (cirBlockData, offset, level) => {
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  try {
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- const data = cirBlockData.slice(offset);
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+ const data = cirBlockData.subarray(offset);
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  const p = this.leafParser.parse(data).result;
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  if (p.blocksToFetch) {
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  blocksToFetch = blocksToFetch.concat(p.blocksToFetch.filter(filterFeats).map((l) => ({
@@ -220,7 +220,7 @@ class BlockView {
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  const features = [];
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  let currOffset = startOffset;
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  while (currOffset < data.byteLength) {
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- const res = this.summaryParser.parse(data.slice(currOffset));
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+ const res = this.summaryParser.parse(data.subarray(currOffset));
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  features.push(res.result);
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  currOffset += res.offset;
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  }
@@ -244,7 +244,7 @@ class BlockView {
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  const items = [];
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  let currOffset = startOffset;
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  while (currOffset < data.byteLength) {
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- const res = this.bigBedParser.parse(data.slice(currOffset));
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+ const res = this.bigBedParser.parse(data.subarray(currOffset));
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  res.result.uniqueId = `bb-${offset + currOffset}`;
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  items.push(res.result);
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  currOffset += res.offset;
@@ -254,7 +254,7 @@ class BlockView {
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  : items;
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  }
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  parseBigWigBlock(bytes, startOffset, request) {
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- const data = bytes.slice(startOffset);
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+ const data = bytes.subarray(startOffset);
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  const results = this.bigWigParser.parse(data).result;
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  const { items, itemSpan, itemStep, blockStart, blockType } = results;
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  if (blockType === BIG_WIG_TYPE_FSTEP) {
@@ -290,7 +290,7 @@ class BlockView {
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  let blockOffset = block.offset - blockGroup.offset;
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  let resultData = data;
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  if (isCompressed) {
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- resultData = (0, unzip_1.unzip)(data.slice(blockOffset));
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+ resultData = (0, unzip_1.unzip)(data.subarray(blockOffset));
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  blockOffset = 0;
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  }
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  (0, util_1.checkAbortSignal)(signal);
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@gmod/bbi",
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- "version": "1.0.32",
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+ "version": "1.0.33",
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  "description": "Parser for BigWig/BigBed files",
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  "license": "MIT",
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  "repository": "GMOD/bbi-js",