@gmod/cram - npm Package Compare versions

Comparing version 1.4.0 to 1.4.1

dist/indexedCramFile.js

@@ -93,3 +93,3 @@ 'use strict';
 
-        var seqId, slices, totalSize, filter, sliceResults, ret, readNames, readIds, _i, name, id, unmatedPairs, matePromises, _i2, _name, mateSlices, mateBlocks, mateChunks, i, _mateChunks, mateRecordPromises, mateFeatPromises, newMateFeats, newMates;
+        var seqId, slices, totalSize, filter, sliceResults, ret, readNames, readIds, _i, name, id, unmatedPairs, matePromises, _i2, _name, mateSlices, mateBlocks, mateChunks, i, _mateChunks, mateRecordPromises, mateFeatPromises, mateTotalSize, newMateFeats, newMates;
 
@@ -100,4 +100,8 @@ return _regenerator2.default.wrap(function _callee$(_context) {
               case 0:
+                opts.viewAsPairs = opts.viewAsPairs || false;
+                opts.pairAcrossChr = opts.pairAcrossChr || false;
+                opts.maxInsertSize = opts.maxInsertSize || 200000;
+
                 if (!(typeof seq === 'string')) {
-                  _context.next = 2;
+                  _context.next = 5;
                   break;
@@ -108,8 +112,8 @@ }
 
-              case 2:
+              case 5:
                 seqId = seq;
-                _context.next = 5;
+                _context.next = 8;
                 return this.index.getEntriesForRange(seqId, start, end);
 
-              case 5:
+              case 8:
                 slices = _context.sent;
@@ -123,3 +127,3 @@ totalSize = slices.map(function (s) {
                 if (!(totalSize > this.fetchSizeLimit)) {
-                  _context.next = 9;
+                  _context.next = 12;
                   break;
@@ -130,3 +134,3 @@ }
 
-              case 9:
+              case 12:
 
@@ -140,3 +144,3 @@ // TODO: do we need to merge or de-duplicate the blocks?
 
-                _context.next = 12;
+                _context.next = 15;
                 return _promise2.default.all(slices.map(function (slice) {
@@ -146,3 +150,3 @@ return _this.getRecordsInSlice(slice, filter);
 
-              case 12:
+              case 15:
                 sliceResults = _context.sent;
@@ -152,3 +156,3 @@ ret = (_Array$prototype = Array.prototype).concat.apply(_Array$prototype, (0, _toConsumableArray3.default)(sliceResults));
                 if (!opts.viewAsPairs) {
-                  _context.next = 35;
+                  _context.next = 41;
                   break;
@@ -182,3 +186,3 @@ }
 
-                  if (unmatedPairs[_name] && (ret[_i2].mate.sequenceId == seqId || opts.pairAcrossChr)) {
+                  if (unmatedPairs[_name] && (ret[_i2].mate.sequenceId == seqId || opts.pairAcrossChr) && Math.abs(ret[_i2].alignmentStart - ret[_i2].mate.alignmentStart) < opts.maxInsertSize) {
                     mateSlices = this.index.getEntriesForRange(ret[_i2].mate.sequenceId, ret[_i2].mate.alignmentStart, ret[_i2].mate.alignmentStart + 1);
@@ -189,6 +193,6 @@
                 }
-                _context.next = 24;
+                _context.next = 27;
                 return _promise2.default.all(matePromises);
 
-              case 24:
+              case 27:
                 mateBlocks = _context.sent;
@@ -209,4 +213,17 @@ mateChunks = [];
                 mateFeatPromises = [];
+                mateTotalSize = mateChunks.map(function (s) {
+                  return s.sliceBytes;
+                }).reduce(function (a, b) {
+                  return a + b;
+                }, 0);
 
+                if (!(mateTotalSize > this.fetchSizeLimit)) {
+                  _context.next = 36;
+                  break;
+                }
 
+                throw new Error('mate data size of ' + mateTotalSize.toLocaleString() + ' bytes exceeded fetch size limit of ' + this.fetchSizeLimit.toLocaleString() + ' bytes');
+
+              case 36:
+
                 mateChunks.forEach(function (c) {
@@ -233,6 +250,6 @@ var recordPromise = _this.cram.featureCache.get(c.toString());
                 });
-                _context.next = 33;
+                _context.next = 39;
                 return _promise2.default.all(mateFeatPromises);
 
-              case 33:
+              case 39:
                 newMateFeats = _context.sent;
@@ -248,6 +265,6 @@
 
-              case 35:
+              case 41:
                 return _context.abrupt('return', ret);
 
-              case 36:
+              case 42:
               case 'end':
@@ -254,0 +271,0 @@ return _context.stop();

package.json

 {
   "name": "@gmod/cram",
-  "version": "1.4.0",
+  "version": "1.4.1",
   "description": "read CRAM files with pure Javascript",
@@ -5,0 +5,0 @@ "license": "MIT",

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Found 1 instance in 1 package

Fixed alerts

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License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

New author

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A new npm collaborator published a version of the package for the first time. New collaborators are usually benign additions to a project, but do indicate a change to the security surface area of a package.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

219825

increased by0.39%

Lines of code

4786

increased by0.29%

Number of medium supply chain risk alerts

4

decreased by-20%

No dependency changes