@jbrowse/plugin-alignments 1.7.7 → 1.7.8

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js

@@ -57,36 +57,17 @@ function isInterbase(type) {
 function inc(bin, strand, type, field) {
   var thisBin = bin[type][field];
 
-  if (!thisBin) {
+  if (thisBin === undefined) {
     thisBin = bin[type][field] = {
       total: 0,
-      strands: {
-        '-1': 0,
-        '0': 0,
-        '1': 0
-      }
+      '-1': 0,
+      '0': 0,
+      '1': 0
     };
   }
 
   thisBin.total++;
-  thisBin.strands[strand]++;
-} // eslint-disable-next-line @typescript-eslint/no-explicit-any
-
-
-function dec(bin, strand, type, field) {
-  if (!bin[type][field]) {
-    bin[type][field] = {
-      total: 0,
-      strands: {
-        '-1': 0,
-        '0': 0,
-        '1': 0
-      }
-    };
-  }
-
-  bin[type][field].total--;
-  bin[type][field].strands[strand]--;
+  thisBin[strand]++;
 }
 
 var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
@@ -396,36 +377,43 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
                 _loop = function _loop(i) {
                   var feature = features[i];
-                  var ops = (0, _MismatchParser.parseCigar)(feature.get('CIGAR'));
                   var fstart = feature.get('start');
                   var fend = feature.get('end');
                   var fstrand = feature.get('strand');
 
-                  for (var j = fstart; j < fend; j++) {
+                  for (var j = fstart; j < fend + 1; j++) {
                     var _i = j - region.start;
 
                     if (_i >= 0 && _i < binMax) {
-                      var bin = bins[_i] || {
-                        total: 0,
-                        lowqual: {},
-                        cov: {},
-                        delskips: {},
-                        noncov: {},
-                        ref: {}
-                      };
+                      if (bins[_i] === undefined) {
+                        bins[_i] = {
+                          total: 0,
+                          ref: 0,
+                          '-1': 0,
+                          '0': 0,
+                          '1': 0,
+                          lowqual: {},
+                          cov: {},
+                          delskips: {},
+                          noncov: {}
+                        };
+                      }
 
                       if (j !== fend) {
-                        bin.total++;
-                        inc(bin, fstrand, 'ref', 'ref');
+                        bins[_i].total++;
+                        bins[_i].ref++;
+                        bins[_i][fstrand]++;
                       }
-
-                      bins[_i] = bin;
                     }
                   }
 
                   if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
                     var seq = feature.get('seq');
                     var mm = (0, _util.getTagAlt)(feature, 'MM', 'Mm') || '';
+                    var ops = (0, _MismatchParser.parseCigar)(feature.get('CIGAR'));
+
+                    var _fend = feature.get('end');
+
                     (0, _MismatchParser.getModificationPositions)(mm, seq, fstrand).forEach(function (_ref4) {
                       var type = _ref4.type,
                           positions = _ref4.positions;
@@ -439,9 +427,14 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                           var pos = _step.value;
                           var epos = pos + fstart - region.start;
 
-                          if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
-                            var _bin = bins[epos];
-                            inc(_bin, fstrand, 'cov', mod);
+                          if (epos >= 0 && epos < bins.length && pos + fstart < _fend) {
+                            var bin = bins[epos];
+
+                            if (bin) {
+                              inc(bin, fstrand, 'cov', mod);
+                            } else {
+                              console.warn('Undefined position in modifications snpcoverage encountered');
+                            }
                           }
                         }
                       } catch (err) {
@@ -462,13 +455,16 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                     var _mm = (0, _util.getTagAlt)(feature, 'MM', 'Mm') || '';
 
                     var methBins = new Array(region.end - region.start).fill(0);
+
+                    var _ops = (0, _MismatchParser.parseCigar)(feature.get('CIGAR'));
+
                     (0, _MismatchParser.getModificationPositions)(_mm, _seq, fstrand).forEach(function (_ref5) {
                       var type = _ref5.type,
                           positions = _ref5.positions;
 
                       // we are processing methylation
                       if (type === 'm') {
-                        var _iterator2 = _createForOfIteratorHelper((0, _MismatchParser.getNextRefPos)(ops, positions)),
+                        var _iterator2 = _createForOfIteratorHelper((0, _MismatchParser.getNextRefPos)(_ops, positions)),
                             _step2;
 
                         try {
@@ -496,80 +492,80 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
                         var l2 = regionSeq[_i2 + 1].toLowerCase();
 
-                        var _bin2 = bins[_i2];
+                        var bin = bins[_i2];
                         var bin1 = bins[_i2 + 1]; // color
 
                         if (l1 === 'c' && l2 === 'g') {
                           if (methBins[_i2] || methBins[_i2 + 1]) {
-                            inc(_bin2, fstrand, 'cov', 'meth');
+                            inc(bin, fstrand, 'cov', 'meth');
                             inc(bin1, fstrand, 'cov', 'meth');
-                            dec(_bin2, fstrand, 'ref', 'ref');
-                            dec(bin1, fstrand, 'ref', 'ref');
+                            bins[_i2].ref--;
+                            bins[_i2][fstrand]--;
+                            bins[_i2 + 1].ref--;
+                            bins[_i2 + 1][fstrand]--;
                           } else {
-                            inc(_bin2, fstrand, 'cov', 'unmeth');
+                            inc(bin, fstrand, 'cov', 'unmeth');
                             inc(bin1, fstrand, 'cov', 'unmeth');
-                            dec(_bin2, fstrand, 'ref', 'ref');
-                            dec(bin1, fstrand, 'ref', 'ref');
+                            bins[_i2].ref--;
+                            bins[_i2][fstrand]--;
+                            bins[_i2 + 1].ref--;
+                            bins[_i2 + 1][fstrand]--;
                           }
                         }
                       }
                     }
                   } // normal SNP based coloring
-                  else {
-                    var mismatches = feature.get('mismatches');
 
-                    if (mismatches) {
-                      for (var _i3 = 0; _i3 < mismatches.length; _i3++) {
-                        var mismatch = mismatches[_i3];
-                        var mstart = fstart + mismatch.start;
 
-                        for (var _j2 = mstart; _j2 < mstart + mismatchLen(mismatch); _j2++) {
-                          var epos = _j2 - region.start;
+                  var mismatches = feature.get('mismatches') || [];
+                  var colorSNPs = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'modifications' && (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'methylation';
 
-                          if (epos >= 0 && epos < bins.length) {
-                            var _bin3 = bins[epos];
-                            var base = mismatch.base,
-                                type = mismatch.type;
-                            var interbase = isInterbase(type);
+                  for (var _i3 = 0; _i3 < mismatches.length; _i3++) {
+                    var mismatch = mismatches[_i3];
+                    var mstart = fstart + mismatch.start;
+                    var mlen = mismatchLen(mismatch);
+                    var mend = mstart + mlen;
 
-                            if (!interbase) {
-                              dec(_bin3, fstrand, 'ref', 'ref');
-                            } else {
-                              inc(_bin3, fstrand, 'noncov', type);
-                            }
+                    for (var _j2 = mstart; _j2 < mstart + mlen; _j2++) {
+                      var epos = _j2 - region.start;
 
-                            if (type === 'deletion' || type === 'skip') {
-                              inc(_bin3, fstrand, 'delskips', type);
-                              _bin3.total--;
-                            } else if (!interbase) {
-                              inc(_bin3, fstrand, 'cov', base);
-                            }
-                          }
-                        }
-                      }
+                      if (epos >= 0 && epos < bins.length) {
+                        var _bin = bins[epos];
+                        var base = mismatch.base,
+                            type = mismatch.type;
+                        var interbase = isInterbase(type);
 
-                      mismatches.filter(function (mismatch) {
-                        return mismatch.type === 'skip';
-                      }).forEach(function (mismatch) {
-                        var mstart = feature.get('start') + mismatch.start;
-                        var start = mstart;
-                        var end = mstart + mismatch.length;
-                        var strand = feature.get('strand');
-                        var hash = "".concat(start, "_").concat(end, "_").concat(strand);
-
-                        if (!skipmap[hash]) {
-                          skipmap[hash] = {
-                            feature: feature,
-                            start: start,
-                            end: end,
-                            strand: strand,
-                            xs: (0, _util.getTag)(feature, 'XS') || (0, _util.getTag)(feature, 'TS'),
-                            score: 1
-                          };
+                        if (!interbase) {
+                          _bin.ref--;
+                          _bin[fstrand]--;
                         } else {
-                          skipmap[hash].score++;
+                          inc(_bin, fstrand, 'noncov', type);
                         }
-                      });
+
+                        if (type === 'deletion' || type === 'skip') {
+                          inc(_bin, fstrand, 'delskips', type);
+                          _bin.total--;
+                        } else if (!interbase && colorSNPs) {
+                          inc(_bin, fstrand, 'cov', base);
+                        }
+                      }
+                    }
+
+                    if (mismatch.type === 'skip') {
+                      var hash = "".concat(mstart, "_").concat(mend, "_").concat(fstrand);
+
+                      if (skipmap[hash] === undefined) {
+                        skipmap[hash] = {
+                          feature: feature,
+                          start: mstart,
+                          end: mend,
+                          strand: fstrand,
+                          xs: (0, _util.getTag)(feature, 'XS') || (0, _util.getTag)(feature, 'TS'),
+                          score: 0
+                        };
+                      }
+
+                      skipmap[hash].score++;
                     }
                   }
                 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "1.7.7",
+  "version": "1.7.8",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -35,7 +35,7 @@
   "dependencies": {
     "@babel/runtime": "^7.17.9",
     "@gmod/bam": "^1.1.15",
-    "@gmod/cram": "^1.6.1",
+    "@gmod/cram": "^1.6.4",
     "@material-ui/icons": "^4.9.1",
     "color": "^3.1.2",
     "copy-to-clipboard": "^3.3.1",
@@ -57,5 +57,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "2c26e04ae942c380bf2f5b79ef7a49cc32b7bfed"
+  "gitHead": "b429fa2bb5734fc8a5380988f6dfdd3f7a41a39f"
 }

package/src/BamAdapter/BamAdapter.ts

@@ -171,7 +171,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         flagInclude: number
         flagExclude: number
         tagFilter: { tag: string; value: unknown }
-        name: string
+        readName: string
       }
     },
   ) {
@@ -187,7 +187,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         flagInclude = 0,
         flagExclude = 0,
         tagFilter,
-        name,
+        readName,
       } = filterBy || {}
 
       for (const record of records) {
@@ -214,7 +214,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
           }
         }
 
-        if (name && record.get('name') !== name) {
+        if (readName && record.get('name') !== readName) {
           continue
         }
 

package/src/BamAdapter/MismatchParser.test.ts

@@ -233,17 +233,15 @@ test('clipping', () => {
   ])
 })
 
-test('getNextRefPos basic', () => {
+test('getNextRefPos test 1', () => {
   const cigar = parseCigar('10S10M1I4M1D15M')
   const iter = getNextRefPos(cigar, [5, 10, 15, 20, 25, 30, 35])
-  const [...vals] = iter
-  expect(vals).toEqual([-5, 0, 5, 10, 14, 20, 25])
+  expect([...iter]).toEqual([0, 5, 15, 20, 25])
 })
-test('getNextRefPos with many indels', () => {
-  const cigar = parseCigar('10S4M1D1IM10')
+test('getNextRefPos test 2', () => {
+  const cigar = parseCigar('10S15M')
   const iter = getNextRefPos(cigar, [5, 10, 15])
-  const [...vals] = iter
-  expect(vals).toEqual([-5, 0, 5])
+  expect([...iter]).toEqual([0, 5])
 })
 
 test('getModificationPositions', () => {

package/src/BamAdapter/MismatchParser.ts

@@ -232,26 +232,32 @@ export function getMismatches(
 // get relative reference sequence positions for positions given relative to
 // the read sequence
 export function* getNextRefPos(cigarOps: string[], positions: number[]) {
-  let cigarIdx = 0
   let readPos = 0
   let refPos = 0
+  let currPos = 0
 
-  for (let i = 0; i < positions.length; i++) {
-    const pos = positions[i]
-    for (; cigarIdx < cigarOps.length && readPos < pos; cigarIdx += 2) {
-      const len = +cigarOps[cigarIdx]
-      const op = cigarOps[cigarIdx + 1]
-      if (op === 'S' || op === 'I') {
-        readPos += len
-      } else if (op === 'D' || op === 'N') {
-        refPos += len
-      } else if (op === 'M' || op === 'X' || op === '=') {
-        readPos += len
-        refPos += len
+  for (let i = 0; i < cigarOps.length && currPos < positions.length; i += 2) {
+    const len = +cigarOps[i]
+    const op = cigarOps[i + 1]
+    if (op === 'S' || op === 'I') {
+      for (let i = 0; i < len && currPos < positions.length; i++) {
+        if (positions[currPos] === readPos + i) {
+          currPos++
+        }
+      }
+      readPos += len
+    } else if (op === 'D' || op === 'N') {
+      refPos += len
+    } else if (op === 'M' || op === 'X' || op === '=') {
+      for (let i = 0; i < len && currPos < positions.length; i++) {
+        if (positions[currPos] === readPos + i) {
+          yield refPos + i
+          currPos++
+        }
       }
+      readPos += len
+      refPos += len
     }
-
-    yield positions[i] - readPos + refPos
   }
 }
 export function getModificationPositions(
@@ -260,54 +266,59 @@ export function getModificationPositions(
   fstrand: number,
 ) {
   const seq = fstrand === -1 ? revcom(fseq) : fseq
-  return mm
-    .split(';')
-    .filter(mod => !!mod)
-    .map(mod => {
-      const [basemod, ...skips] = mod.split(',')
+  const mods = mm.split(';').filter(mod => !!mod)
+  const result = []
+  for (let i = 0; i < mods.length; i++) {
+    const mod = mods[i]
+    const [basemod, ...skips] = mod.split(',')
 
-      // regexes based on parse_mm.pl from hts-specs
-      const matches = basemod.match(/([A-Z])([-+])([^,.?]+)([.?])?/)
-      if (!matches) {
-        throw new Error('bad format for MM tag')
-      }
-      const [, base, strand, typestr] = matches
+    // regexes based on parse_mm.pl from hts-specs
+    const matches = basemod.match(/([A-Z])([-+])([^,.?]+)([.?])?/)
+    if (!matches) {
+      throw new Error('bad format for MM tag')
+    }
+    const [, base, strand, typestr] = matches
 
-      // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so
-      // split, and they can also be chemical codes (ChEBI) e.g. C+16061
-      const types = typestr.split(/(\d+|.)/).filter(f => !!f)
+    // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so
+    // split, and they can also be chemical codes (ChEBI) e.g. C+16061
+    const types = typestr.split(/(\d+|.)/).filter(f => !!f)
 
-      if (strand === '-') {
-        console.warn('unsupported negative strand modifications')
-        // make sure to return a somewhat matching type even in this case
-        return { type: 'unsupported', positions: [] }
-      }
+    if (strand === '-') {
+      console.warn('unsupported negative strand modifications')
+      // make sure to return a somewhat matching type even in this case
+      result.push({ type: 'unsupported', positions: [] as number[] })
+    }
 
-      // this logic also based on parse_mm.pl from hts-specs is that in the
-      // sequence of the read, if we have a modification type e.g. C+m;2 and a
-      // sequence ACGTACGTAC we skip the two instances of C and go to the last
-      // C
-      return types.map(type => {
-        let i = 0
-        return {
-          type,
-          positions: skips
-            .map(score => +score)
-            .map(delta => {
-              do {
-                if (base === 'N' || base === seq[i]) {
-                  delta--
-                }
-                i++
-              } while (delta >= 0 && i < seq.length)
-              const temp = i - 1
-              return fstrand === -1 ? seq.length - 1 - temp : temp
-            })
-            .sort((a, b) => a - b),
-        }
+    // this logic also based on parse_mm.pl from hts-specs is that in the
+    // sequence of the read, if we have a modification type e.g. C+m;2 and a
+    // sequence ACGTACGTAC we skip the two instances of C and go to the last
+    // C
+    for (let j = 0; j < types.length; j++) {
+      const type = types[j]
+      let i = 0
+      const positions = []
+      for (let k = 0; k < skips.length; k++) {
+        let delta = +skips[k]
+        do {
+          if (base === 'N' || base === seq[i]) {
+            delta--
+          }
+          i++
+        } while (delta >= 0 && i < seq.length)
+
+        const temp = i - 1
+        positions.push(fstrand === -1 ? seq.length - 1 - temp : temp)
+      }
+      if (fstrand === -1) {
+        positions.sort((a, b) => a - b)
+      }
+      result.push({
+        type,
+        positions,
       })
-    })
-    .flat()
+    }
+  }
+  return result
 }
 
 export function getModificationTypes(mm: string) {

package/src/CramAdapter/CramAdapter.ts

@@ -20,6 +20,13 @@ interface Header {
   readGroups?: number[]
 }
 
+interface FilterBy {
+  flagInclude: number
+  flagExclude: number
+  tagFilter: { tag: string; value: unknown }
+  readName: string
+}
+
 export default class CramAdapter extends BaseFeatureDataAdapter {
   samHeader: Header = {}
 
@@ -206,12 +213,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
   getFeatures(
     region: Region & { originalRefName?: string },
     opts?: BaseOptions & {
-      filterBy: {
-        flagInclude: number
-        flagExclude: number
-        tagFilter: { tag: string; value: unknown }
-        name: string
-      }
+      filterBy: FilterBy
     },
   ) {
     const { signal, filterBy, statusCallback = () => {} } = opts || {}
@@ -234,7 +236,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
           flagInclude = 0,
           flagExclude = 0,
           tagFilter,
-          name,
+          readName,
         } = filterBy || {}
 
         // eslint-disable-next-line @typescript-eslint/no-explicit-any
@@ -251,9 +253,11 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
           })
         }
 
-        if (name) {
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any
-          filtered = filtered.filter((record: any) => record.name === name)
+        if (readName) {
+          filtered = filtered.filter(
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            (record: any) => record.readName === readName,
+          )
         }
 
         // eslint-disable-next-line @typescript-eslint/no-explicit-any