@jbrowse/plugin-alignments 1.7.9 → 2.0.0

package/dist/PileupRenderer/configSchema.js

@@ -1,72 +1,66 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _default = (0, _configuration.ConfigurationSchema)('PileupRenderer', {
-  // default magenta here is used to detect the user has not customized this
-  color: {
-    type: 'color',
-    description: 'the color of each feature in a pileup alignment',
-    defaultValue: '#f0f',
-    contextVariable: ['feature']
-  },
-  orientationType: {
-    type: 'stringEnum',
-    model: _mobxStateTree.types.enumeration('orientationType', ['fr', 'rf', 'ff']),
-    defaultValue: 'fr',
-    description: 'read sequencer orienation. fr is normal "reads pointing at each other ---> <--- while some other sequencers can use other options'
-  },
-  displayMode: {
-    type: 'stringEnum',
-    model: _mobxStateTree.types.enumeration('displayMode', ['normal', 'compact', 'collapse']),
-    description: 'Alternative display modes',
-    defaultValue: 'normal'
-  },
-  minSubfeatureWidth: {
-    type: 'number',
-    description: 'the minimum width in px for a pileup mismatch feature. use for increasing/decreasing mismatch marker widths when zoomed out, e.g. 0 or 1',
-    defaultValue: 0.7
-  },
-  maxHeight: {
-    type: 'integer',
-    description: 'the maximum height to be used in a pileup rendering',
-    defaultValue: 1200
-  },
-  maxClippingSize: {
-    type: 'integer',
-    description: 'the max clip size to be used in a pileup rendering',
-    defaultValue: 10000
-  },
-  height: {
-    type: 'number',
-    description: 'the height of each feature in a pileup alignment',
-    defaultValue: 7,
-    contextVariable: ['feature']
-  },
-  noSpacing: {
-    type: 'boolean',
-    description: 'remove spacing between features',
-    defaultValue: false
-  },
-  largeInsertionIndicatorScale: {
-    type: 'number',
-    description: 'scale at which to draw the large insertion indicators (bp/pixel)',
-    defaultValue: 10
-  },
-  mismatchAlpha: {
-    type: 'boolean',
-    defaultValue: false,
-    description: 'Fade low quality mismatches'
-  }
-}, {
-  explicitlyTyped: true
-});
-
-exports.default = _default;
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+var mobx_state_tree_1 = require("mobx-state-tree");
+exports.default = (0, configuration_1.ConfigurationSchema)('PileupRenderer', {
+    // default magenta here is used to detect the user has not customized this
+    color: {
+        type: 'color',
+        description: 'the color of each feature in a pileup alignment',
+        defaultValue: '#f0f',
+        contextVariable: ['feature'],
+    },
+    orientationType: {
+        type: 'stringEnum',
+        model: mobx_state_tree_1.types.enumeration('orientationType', ['fr', 'rf', 'ff']),
+        defaultValue: 'fr',
+        description: 'read sequencer orienation. fr is normal "reads pointing at each other ---> <--- while some other sequencers can use other options',
+    },
+    displayMode: {
+        type: 'stringEnum',
+        model: mobx_state_tree_1.types.enumeration('displayMode', [
+            'normal',
+            'compact',
+            'collapse',
+        ]),
+        description: 'Alternative display modes',
+        defaultValue: 'normal',
+    },
+    minSubfeatureWidth: {
+        type: 'number',
+        description: 'the minimum width in px for a pileup mismatch feature. use for increasing/decreasing mismatch marker widths when zoomed out, e.g. 0 or 1',
+        defaultValue: 0.7,
+    },
+    maxHeight: {
+        type: 'integer',
+        description: 'the maximum height to be used in a pileup rendering',
+        defaultValue: 1200,
+    },
+    maxClippingSize: {
+        type: 'integer',
+        description: 'the max clip size to be used in a pileup rendering',
+        defaultValue: 10000,
+    },
+    height: {
+        type: 'number',
+        description: 'the height of each feature in a pileup alignment',
+        defaultValue: 7,
+        contextVariable: ['feature'],
+    },
+    noSpacing: {
+        type: 'boolean',
+        description: 'remove spacing between features',
+        defaultValue: false,
+    },
+    largeInsertionIndicatorScale: {
+        type: 'number',
+        description: 'scale at which to draw the large insertion indicators (bp/pixel)',
+        defaultValue: 10,
+    },
+    mismatchAlpha: {
+        type: 'boolean',
+        defaultValue: false,
+        description: 'Fade low quality mismatches',
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/dist/PileupRenderer/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/PileupRenderer/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AACjE,mDAAuC;AAEvC,kBAAe,IAAA,mCAAmB,EAChC,gBAAgB,EAChB;IACE,0EAA0E;IAC1E,KAAK,EAAE;QACL,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,iDAAiD;QAC9D,YAAY,EAAE,MAAM;QACpB,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD,eAAe,EAAE;QACf,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,iBAAiB,EAAE,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,CAAC;QAC/D,YAAY,EAAE,IAAI;QAClB,WAAW,EACT,mIAAmI;KACtI;IACD,WAAW,EAAE;QACX,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,aAAa,EAAE;YACtC,QAAQ;YACR,SAAS;YACT,UAAU;SACX,CAAC;QACF,WAAW,EAAE,2BAA2B;QACxC,YAAY,EAAE,QAAQ;KACvB;IACD,kBAAkB,EAAE;QAClB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,0IAA0I;QAC5I,YAAY,EAAE,GAAG;KAClB;IACD,SAAS,EAAE;QACT,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,qDAAqD;QAClE,YAAY,EAAE,IAAI;KACnB;IACD,eAAe,EAAE;QACf,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,oDAAoD;QACjE,YAAY,EAAE,KAAK;KACpB;IACD,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,kDAAkD;QAC/D,YAAY,EAAE,CAAC;QACf,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD,SAAS,EAAE;QACT,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,iCAAiC;QAC9C,YAAY,EAAE,KAAK;KACpB;IACD,4BAA4B,EAAE;QAC5B,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,kEAAkE;QACpE,YAAY,EAAE,EAAE;KACjB;IACD,aAAa,EAAE;QACb,IAAI,EAAE,SAAS;QACf,YAAY,EAAE,KAAK;QACnB,WAAW,EAAE,6BAA6B;KAC3C;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/PileupRenderer/index.js

@@ -1,25 +1,20 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = register;
-
-var _PileupRenderer = _interopRequireDefault(require("./PileupRenderer"));
-
-var _PileupRendering = _interopRequireDefault(require("./components/PileupRendering"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var PileupRenderer_1 = __importDefault(require("./PileupRenderer"));
+var PileupRendering_1 = __importDefault(require("./components/PileupRendering"));
+var configSchema_1 = __importDefault(require("./configSchema"));
 function register(pluginManager) {
-  pluginManager.addRendererType(function () {
-    return new _PileupRenderer.default({
-      name: 'PileupRenderer',
-      ReactComponent: _PileupRendering.default,
-      configSchema: _configSchema.default,
-      pluginManager: pluginManager
+    pluginManager.addRendererType(function () {
+        return new PileupRenderer_1.default({
+            name: 'PileupRenderer',
+            ReactComponent: PileupRendering_1.default,
+            configSchema: configSchema_1.default,
+            pluginManager: pluginManager,
+        });
     });
-  });
-}
+}
+exports.default = register;
+//# sourceMappingURL=index.js.map

package/dist/PileupRenderer/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/PileupRenderer/index.ts"],"names":[],"mappings":";;;;;AACA,oEAA6C;AAC7C,iFAAyD;AACzD,gEAAyC;AAEzC,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,eAAe,CAC3B;QACE,OAAA,IAAI,wBAAc,CAAC;YACjB,IAAI,EAAE,gBAAgB;YACtB,cAAc,2BAAA;YACd,YAAY,wBAAA;YACZ,aAAa,eAAA;SACd,CAAC;IALF,CAKE,CACL,CAAA;AACH,CAAC;AAVD,2BAUC"}

package/dist/PileupRenderer/sortUtil.js

@@ -1,112 +1,88 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
+Object.defineProperty(exports, "__esModule", { value: true });
 exports.sortFeature = void 0;
-
-var _range = require("@jbrowse/core/util/range");
-
-var sortFeature = function sortFeature(features, sortedBy) {
-  var featureArray = Array.from(features.values());
-  var featuresInCenterLine = [];
-  var featuresOutsideCenter = [];
-  var pos = sortedBy.pos,
-      type = sortedBy.type; // only sort on features that intersect center line, append those outside post-sort
-
-  featureArray.forEach(function (innerArray) {
-    var feature = innerArray;
-    var start = feature.get('start');
-    var end = feature.get('end');
-
-    if ((0, _range.doesIntersect2)(pos - 1, pos, start, end)) {
-      featuresInCenterLine.push(innerArray);
-    } else {
-      featuresOutsideCenter.push(innerArray);
-    }
-  });
-  var isCram = featureArray.length ? featureArray[0].get('tags') : false;
-
-  switch (type) {
-    case 'Start location':
-      {
-        featuresInCenterLine.sort(function (a, b) {
-          return a.get('start') - b.get('start');
-        });
-        break;
-      }
-
-    case 'tag':
-      {
-        var tag = sortedBy.tag;
-
-        var getTag = function getTag(f, t) {
-          return isCram ? f.get('tags')[t] : f.get(t);
-        };
-
-        var isString = featuresInCenterLine[0] && typeof getTag(featuresInCenterLine[0], tag) === 'string';
-
-        if (isString) {
-          featuresInCenterLine.sort(function (a, b) {
-            return getTag(b, tag).localeCompare(getTag(a, tag));
-          });
-        } else {
-          featuresInCenterLine.sort(function (a, b) {
-            return (getTag(b, tag) || 0) - (getTag(a, tag) || 0);
-          });
+var range_1 = require("@jbrowse/core/util/range");
+var sortFeature = function (features, sortedBy) {
+    var featureArray = Array.from(features.values());
+    var featuresInCenterLine = [];
+    var featuresOutsideCenter = [];
+    var pos = sortedBy.pos, type = sortedBy.type;
+    // only sort on features that intersect center line, append those outside post-sort
+    featureArray.forEach(function (innerArray) {
+        var feature = innerArray;
+        var start = feature.get('start');
+        var end = feature.get('end');
+        if ((0, range_1.doesIntersect2)(pos - 1, pos, start, end)) {
+            featuresInCenterLine.push(innerArray);
+        }
+        else {
+            featuresOutsideCenter.push(innerArray);
         }
-
-        break;
-      }
-    // first sort all mismatches, then all reference bases at the end
-
-    case 'Base pair':
-      {
-        var baseSortArray = [];
-        featuresInCenterLine.forEach(function (feature) {
-          var mismatches = feature.get('mismatches');
-          mismatches.forEach(function (mismatch) {
-            var start = feature.get('start');
-            var offset = start + mismatch.start + 1;
-            var consuming = mismatch.type === 'insertion' || mismatch.type === 'softclip';
-            var len = consuming ? 0 : mismatch.length;
-
-            if (pos >= offset && pos < offset + len) {
-              baseSortArray.push([feature.id(), mismatch]);
+    });
+    var isCram = featureArray.length ? featureArray[0].get('tags') : false;
+    switch (type) {
+        case 'Start location': {
+            featuresInCenterLine.sort(function (a, b) { return a.get('start') - b.get('start'); });
+            break;
+        }
+        case 'tag': {
+            var tag_1 = sortedBy.tag;
+            var getTag_1 = function (f, t) {
+                return isCram ? f.get('tags')[t] : f.get(t);
+            };
+            var isString = featuresInCenterLine[0] &&
+                typeof getTag_1(featuresInCenterLine[0], tag_1) === 'string';
+            if (isString) {
+                featuresInCenterLine.sort(function (a, b) {
+                    return getTag_1(b, tag_1).localeCompare(getTag_1(a, tag_1));
+                });
+            }
+            else {
+                featuresInCenterLine.sort(function (a, b) { return (getTag_1(b, tag_1) || 0) - (getTag_1(a, tag_1) || 0); });
             }
-          });
-        });
-        var baseMap = new Map(baseSortArray);
-        featuresInCenterLine.sort(function (a, b) {
-          var aMismatch = baseMap.get(a.id());
-          var bMismatch = baseMap.get(b.id());
-          var acode = bMismatch && bMismatch.base.toUpperCase();
-          var bcode = aMismatch && aMismatch.base.toUpperCase();
-
-          if (acode === bcode && acode === '*') {
-            // @ts-ignore
-            return aMismatch.length - bMismatch.length;
-          }
-
-          return (acode ? acode.charCodeAt(0) : 0) - (bcode ? bcode.charCodeAt(0) : 0);
-        });
-        break;
-      }
-    // sorts positive strands then negative strands
-
-    case 'Read strand':
-      {
-        featuresInCenterLine.sort(function (a, b) {
-          return a.get('strand') <= b.get('strand') ? 1 : -1;
-        });
-        break;
-      }
-  }
-
-  var sortedMap = new Map(featuresInCenterLine.concat(featuresOutsideCenter).map(function (feature) {
-    return [feature.id(), feature];
-  }));
-  return sortedMap;
+            break;
+        }
+        // first sort all mismatches, then all reference bases at the end
+        case 'Base pair': {
+            var baseSortArray_1 = [];
+            featuresInCenterLine.forEach(function (feature) {
+                var mismatches = feature.get('mismatches');
+                mismatches.forEach(function (mismatch) {
+                    var start = feature.get('start');
+                    var offset = start + mismatch.start + 1;
+                    var consuming = mismatch.type === 'insertion' || mismatch.type === 'softclip';
+                    var len = consuming ? 0 : mismatch.length;
+                    if (pos >= offset && pos < offset + len) {
+                        baseSortArray_1.push([feature.id(), mismatch]);
+                    }
+                });
+            });
+            var baseMap_1 = new Map(baseSortArray_1);
+            featuresInCenterLine.sort(function (a, b) {
+                var aMismatch = baseMap_1.get(a.id());
+                var bMismatch = baseMap_1.get(b.id());
+                var acode = bMismatch && bMismatch.base.toUpperCase();
+                var bcode = aMismatch && aMismatch.base.toUpperCase();
+                if (acode === bcode && acode === '*') {
+                    // @ts-ignore
+                    return aMismatch.length - bMismatch.length;
+                }
+                return ((acode ? acode.charCodeAt(0) : 0) - (bcode ? bcode.charCodeAt(0) : 0));
+            });
+            break;
+        }
+        // sorts positive strands then negative strands
+        case 'Read strand': {
+            featuresInCenterLine.sort(function (a, b) {
+                return a.get('strand') <= b.get('strand') ? 1 : -1;
+            });
+            break;
+        }
+    }
+    var sortedMap = new Map(featuresInCenterLine
+        .concat(featuresOutsideCenter)
+        .map(function (feature) { return [feature.id(), feature]; }));
+    return sortedMap;
 };
-
-exports.sortFeature = sortFeature;
+exports.sortFeature = sortFeature;
+//# sourceMappingURL=sortUtil.js.map

package/dist/PileupRenderer/sortUtil.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"sortUtil.js","sourceRoot":"","sources":["../../src/PileupRenderer/sortUtil.ts"],"names":[],"mappings":";;;AACA,kDAAyD;AAQlD,IAAM,WAAW,GAAG,UACzB,QAA8B,EAC9B,QAAoB;IAEpB,IAAM,YAAY,GAAG,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAA;IAClD,IAAM,oBAAoB,GAAc,EAAE,CAAA;IAC1C,IAAM,qBAAqB,GAAc,EAAE,CAAA;IACnC,IAAA,GAAG,GAAW,QAAQ,IAAnB,EAAE,IAAI,GAAK,QAAQ,KAAb,CAAa;IAE9B,mFAAmF;IACnF,YAAY,CAAC,OAAO,CAAC,UAAA,UAAU;QAC7B,IAAM,OAAO,GAAG,UAAU,CAAA;QAC1B,IAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QAClC,IAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QAC9B,IAAI,IAAA,sBAAc,EAAC,GAAG,GAAG,CAAC,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,CAAC,EAAE;YAC5C,oBAAoB,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;SACtC;aAAM;YACL,qBAAqB,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;SACvC;IACH,CAAC,CAAC,CAAA;IAEF,IAAM,MAAM,GAAG,YAAY,CAAC,MAAM,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,KAAK,CAAA;IACxE,QAAQ,IAAI,EAAE;QACZ,KAAK,gBAAgB,CAAC,CAAC;YACrB,oBAAoB,CAAC,IAAI,CAAC,UAAC,CAAC,EAAE,CAAC,IAAK,OAAA,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAA/B,CAA+B,CAAC,CAAA;YACpE,MAAK;SACN;QAED,KAAK,KAAK,CAAC,CAAC;YACV,IAAM,KAAG,GAAG,QAAQ,CAAC,GAAa,CAAA;YAClC,IAAM,QAAM,GAAG,UAAC,CAAU,EAAE,CAAS;gBACnC,OAAO,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YAC7C,CAAC,CAAA;YACD,IAAM,QAAQ,GACZ,oBAAoB,CAAC,CAAC,CAAC;gBACvB,OAAO,QAAM,CAAC,oBAAoB,CAAC,CAAC,CAAC,EAAE,KAAG,CAAC,KAAK,QAAQ,CAAA;YAC1D,IAAI,QAAQ,EAAE;gBACZ,oBAAoB,CAAC,IAAI,CAAC,UAAC,CAAC,EAAE,CAAC;oBAC7B,OAAA,QAAM,CAAC,CAAC,EAAE,KAAG,CAAC,CAAC,aAAa,CAAC,QAAM,CAAC,CAAC,EAAE,KAAG,CAAC,CAAC;gBAA5C,CAA4C,CAC7C,CAAA;aACF;iBAAM;gBACL,oBAAoB,CAAC,IAAI,CACvB,UAAC,CAAC,EAAE,CAAC,IAAK,OAAA,CAAC,QAAM,CAAC,CAAC,EAAE,KAAG,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,QAAM,CAAC,CAAC,EAAE,KAAG,CAAC,IAAI,CAAC,CAAC,EAA7C,CAA6C,CACxD,CAAA;aACF;YACD,MAAK;SACN;QAED,iEAAiE;QACjE,KAAK,WAAW,CAAC,CAAC;YAChB,IAAM,eAAa,GAAyB,EAAE,CAAA;YAC9C,oBAAoB,CAAC,OAAO,CAAC,UAAA,OAAO;gBAClC,IAAM,UAAU,GAAe,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;gBACxD,UAAU,CAAC,OAAO,CAAC,UAAA,QAAQ;oBACzB,IAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;oBAClC,IAAM,MAAM,GAAG,KAAK,GAAG,QAAQ,CAAC,KAAK,GAAG,CAAC,CAAA;oBACzC,IAAM,SAAS,GACb,QAAQ,CAAC,IAAI,KAAK,WAAW,IAAI,QAAQ,CAAC,IAAI,KAAK,UAAU,CAAA;oBAC/D,IAAM,GAAG,GAAG,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAA;oBAC3C,IAAI,GAAG,IAAI,MAAM,IAAI,GAAG,GAAG,MAAM,GAAG,GAAG,EAAE;wBACvC,eAAa,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,EAAE,EAAE,EAAE,QAAQ,CAAC,CAAC,CAAA;qBAC7C;gBACH,CAAC,CAAC,CAAA;YACJ,CAAC,CAAC,CAAA;YAEF,IAAM,SAAO,GAAG,IAAI,GAAG,CAAC,eAAa,CAAC,CAAA;YACtC,oBAAoB,CAAC,IAAI,CAAC,UAAC,CAAC,EAAE,CAAC;gBAC7B,IAAM,SAAS,GAAG,SAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAA;gBACrC,IAAM,SAAS,GAAG,SAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAA;gBACrC,IAAM,KAAK,GAAG,SAAS,IAAI,SAAS,CAAC,IAAI,CAAC,WAAW,EAAE,CAAA;gBACvD,IAAM,KAAK,GAAG,SAAS,IAAI,SAAS,CAAC,IAAI,CAAC,WAAW,EAAE,CAAA;gBACvD,IAAI,KAAK,KAAK,KAAK,IAAI,KAAK,KAAK,GAAG,EAAE;oBACpC,aAAa;oBACb,OAAO,SAAS,CAAC,MAAM,GAAG,SAAS,CAAC,MAAM,CAAA;iBAC3C;gBACD,OAAO,CACL,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CACtE,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,MAAK;SACN;QAED,+CAA+C;QAC/C,KAAK,aAAa,CAAC,CAAC;YAClB,oBAAoB,CAAC,IAAI,CAAC,UAAC,CAAC,EAAE,CAAC;gBAC7B,OAAA,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YAA3C,CAA2C,CAC5C,CAAA;YACD,MAAK;SACN;KACF;IAED,IAAM,SAAS,GAAG,IAAI,GAAG,CACvB,oBAAoB;SACjB,MAAM,CAAC,qBAAqB,CAAC;SAC7B,GAAG,CAAC,UAAA,OAAO,IAAI,OAAA,CAAC,OAAO,CAAC,EAAE,EAAE,EAAE,OAAO,CAAC,EAAvB,CAAuB,CAAC,CAC3C,CAAA;IAED,OAAO,SAAS,CAAA;AAClB,CAAC,CAAA;AAnGY,QAAA,WAAW,eAmGvB"}

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts

@@ -19,7 +19,9 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
         };
     }): Promise<{
         bins: {
+            refbase?: string | undefined;
             total: number;
+            all: number;
             ref: number;
             '-1': 0;
             '0': 0;