@jbrowse/plugin-alignments 2.2.2 → 2.3.0

package/dist/{shared.js → shared/index.js}

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getUniqueModificationValues = exports.getUniqueTagValues = void 0;
+exports.FilterModel = exports.getUniqueModificationValues = exports.getUniqueTagValues = void 0;
+const mobx_state_tree_1 = require("mobx-state-tree");
 const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
 async function getUniqueTagValues(self, colorScheme, blocks, opts) {
@@ -30,4 +31,13 @@ async function getUniqueModificationValues(self, adapterConfig, colorScheme, blo
     return values;
 }
 exports.getUniqueModificationValues = getUniqueModificationValues;
-//# sourceMappingURL=shared.js.map
+exports.FilterModel = mobx_state_tree_1.types.model({
+    flagInclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
+    flagExclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 1540),
+    readName: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
+    tagFilter: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.model({
+        tag: mobx_state_tree_1.types.string,
+        value: mobx_state_tree_1.types.string,
+    })),
+});
+//# sourceMappingURL=index.js.map

package/dist/shared/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/shared/index.ts"],"names":[],"mappings":";;;AAAA,qDAA0D;AAE1D,6CAA+C;AAC/C,sDAA2D;AAGpD,KAAK,UAAU,kBAAkB,CACtC,IAAkE,EAClE,WAA2C,EAC3C,MAAgB,EAChB,IAIC;IAED,MAAM,EAAE,UAAU,EAAE,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;IACvC,MAAM,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;IAC9B,MAAM,SAAS,GAAG,IAAA,wBAAe,EAAC,IAAI,CAAC,CAAA;IACvC,MAAM,MAAM,GAAG,MAAM,UAAU,CAAC,IAAI,CAClC,IAAA,wBAAe,EAAC,IAAI,CAAC,EACrB,4BAA4B,EAC5B;QACE,aAAa;QACb,GAAG,EAAE,WAAW,CAAC,GAAG;QACpB,SAAS;QACT,OAAO,EAAE,MAAM,CAAC,aAAa;QAC7B,GAAG,IAAI;KACR,CACF,CAAA;IACD,OAAO,MAAkB,CAAA;AAC3B,CAAC;AAzBD,gDAyBC;AAIM,KAAK,UAAU,2BAA2B,CAC/C,IAEC,EACD,aAAoC,EACpC,WAA2C,EAC3C,MAAgB,EAChB,IAIC;IAED,MAAM,EAAE,UAAU,EAAE,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;IACvC,MAAM,SAAS,GAAG,IAAA,wBAAe,EAAC,IAAI,CAAC,CAAA;IACvC,MAAM,MAAM,GAAG,MAAM,UAAU,CAAC,IAAI,CAClC,SAAS,EACT,+BAA+B,EAC/B;QACE,aAAa;QACb,GAAG,EAAE,WAAW,CAAC,GAAG;QACpB,SAAS;QACT,OAAO,EAAE,MAAM,CAAC,aAAa;QAC7B,GAAG,IAAI;KACR,CACF,CAAA;IACD,OAAO,MAAkB,CAAA;AAC3B,CAAC;AA3BD,kEA2BC;AAEY,QAAA,WAAW,GAAG,uBAAK,CAAC,KAAK,CAAC;IACrC,WAAW,EAAE,uBAAK,CAAC,QAAQ,CAAC,uBAAK,CAAC,MAAM,EAAE,CAAC,CAAC;IAC5C,WAAW,EAAE,uBAAK,CAAC,QAAQ,CAAC,uBAAK,CAAC,MAAM,EAAE,IAAI,CAAC;IAC/C,QAAQ,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,MAAM,CAAC;IACnC,SAAS,EAAE,uBAAK,CAAC,KAAK,CACpB,uBAAK,CAAC,KAAK,CAAC;QACV,GAAG,EAAE,uBAAK,CAAC,MAAM;QACjB,KAAK,EAAE,uBAAK,CAAC,MAAM;KACpB,CAAC,CACH;CACF,CAAC,CAAA"}

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -6,7 +6,7 @@ import { getSession } from '@jbrowse/core/util';
 import copy from 'copy-to-clipboard';
 import clone from 'clone';
 import { FeatureDetails, BaseCard, SimpleValue, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
-import { parseCigar } from '../BamAdapter/MismatchParser';
+import { parseCigar } from '../MismatchParser';
 const useStyles = makeStyles()({
     compact: {
         paddingRight: 0,

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map

@@ -1 +1 @@
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package/esm/AlignmentsTrack/index.js

@@ -19,6 +19,7 @@ export default function register(pm) {
         const configSchema = configSchemaFactory(pm);
         const track = new TrackType({
             name: 'AlignmentsTrack',
+            displayName: 'Alignments track',
             configSchema,
             stateModel: createBaseTrackModel(pm, 'AlignmentsTrack', configSchema),
         });

package/esm/AlignmentsTrack/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/index.ts"],"names":[],"mappings":"AACA,OAAO,SAAS,MAAM,+CAA+C,CAAA;AACrE,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EACL,qBAAqB,EACrB,oBAAoB,GACrB,MAAM,4CAA4C,CAAA;AAEnD;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,mBAAmB,CAAC,aAA4B;IACvD,OAAO,mBAAmB,CACxB,iBAAiB,EACjB,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,qBAAqB,CAAC,aAAa,CAAC;KACxD,CACF,CAAA;AACH,CAAC;AACD,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,EAAiB;IAChD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,mBAAmB,CAAC,EAAE,CAAC,CAAA;QAC5C,MAAM,KAAK,GAAG,IAAI,SAAS,CAAC;YAC1B,IAAI,EAAE,iBAAiB;YACvB,YAAY;YACZ,UAAU,EAAE,oBAAoB,CAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,CAAC;SACtE,CAAC,CAAA;QACF,MAAM,uBAAuB,GAAG,EAAE,CAAC,cAAc,CAAC,yBAAyB,CAAC,CAAA;QAC5E,0EAA0E;QAC1E,yEAAyE;QACzE,qDAAqD;QACrD,KAAK,CAAC,cAAc,CAAC,uBAAuB,CAAC,CAAA;QAC7C,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;AACJ,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/index.ts"],"names":[],"mappings":"AACA,OAAO,SAAS,MAAM,+CAA+C,CAAA;AACrE,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EACL,qBAAqB,EACrB,oBAAoB,GACrB,MAAM,4CAA4C,CAAA;AAEnD;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,mBAAmB,CAAC,aAA4B;IACvD,OAAO,mBAAmB,CACxB,iBAAiB,EACjB,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,qBAAqB,CAAC,aAAa,CAAC;KACxD,CACF,CAAA;AACH,CAAC;AACD,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,EAAiB;IAChD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,mBAAmB,CAAC,EAAE,CAAC,CAAA;QAC5C,MAAM,KAAK,GAAG,IAAI,SAAS,CAAC;YAC1B,IAAI,EAAE,iBAAiB;YACvB,WAAW,EAAE,kBAAkB;YAC/B,YAAY;YACZ,UAAU,EAAE,oBAAoB,CAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,CAAC;SACtE,CAAC,CAAA;QACF,MAAM,uBAAuB,GAAG,EAAE,CAAC,cAAc,CAAC,yBAAyB,CAAC,CAAA;QAC5E,0EAA0E;QAC1E,yEAAyE;QACzE,qDAAqD;QACrD,KAAK,CAAC,cAAc,CAAC,uBAAuB,CAAC,CAAA;QAC7C,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/esm/BamAdapter/BamSlightlyLazyFeature.d.ts

@@ -13,9 +13,8 @@ export default class BamSlightlyLazyFeature implements Feature {
     _get_flags(): string;
     _get_strand(): number;
     _get_pair_orientation(): string | null | undefined;
-    _get_next_seq_id(): number;
-    _get_seq_id(): number;
-    _get_next_refName(): string | undefined;
+    _get_next_ref(): string | undefined;
+    _get_next_pos(): number | undefined;
     _get_next_segment_position(): string | undefined;
     _get_seq(): string;
     qualRaw(): Buffer | undefined;
@@ -28,6 +27,6 @@ export default class BamSlightlyLazyFeature implements Feature {
     children(): undefined;
     pairedFeature(): boolean;
     toJSON(): SimpleFeatureSerialized;
-    _get_mismatches(): import("./MismatchParser").Mismatch[];
+    _get_mismatches(): import("../MismatchParser").Mismatch[];
     _get_clipPos(): number;
 }

package/esm/BamAdapter/BamSlightlyLazyFeature.js

@@ -1,5 +1,5 @@
 // locals
-import { getMismatches } from './MismatchParser';
+import { getClip, getMismatches } from '../MismatchParser';
 export default class BamSlightlyLazyFeature {
     // uses parameter properties to automatically create fields on the class
     // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
@@ -26,20 +26,17 @@ export default class BamSlightlyLazyFeature {
     _get_pair_orientation() {
         return this.record.isPaired() ? this.record.getPairOrientation() : undefined;
     }
-    _get_next_seq_id() {
-        return this.record._next_refid();
-    }
-    _get_seq_id() {
-        // @ts-ignore
-        return this.record._refID;
+    _get_next_ref() {
+        return this.record.isPaired()
+            ? this.adapter.refIdToName(this.record._next_refid())
+            : undefined;
     }
-    _get_next_refName() {
-        return this.adapter.refIdToName(this.record._next_refid());
+    _get_next_pos() {
+        return this.record.isPaired() ? this.record._next_pos() : undefined;
     }
     _get_next_segment_position() {
-        const { record, adapter } = this;
-        return record.isPaired()
-            ? `${adapter.refIdToName(record._next_refid())}:${record._next_pos() + 1}`
+        return this.record.isPaired()
+            ? `${this.adapter.refIdToName(this.record._next_refid())}:${this.record._next_pos() + 1}`
             : undefined;
     }
     _get_seq() {
@@ -55,9 +52,7 @@ export default class BamSlightlyLazyFeature {
             ...new Set(properties
                 .filter(prop => prop.startsWith('_get_') &&
                 prop !== '_get_mismatches' &&
-                prop !== '_get_tags' &&
-                prop !== '_get_next_seq_id' &&
-                prop !== '_get_seq_id')
+                prop !== '_get_tags')
                 .map(methodName => methodName.replace('_get_', ''))
                 .concat(this.record._tags())),
         ];
@@ -100,9 +95,7 @@ export default class BamSlightlyLazyFeature {
     }
     _get_clipPos() {
         const cigar = this.get('CIGAR') || '';
-        return this.get('strand') === -1
-            ? +(cigar.match(/(\d+)[SH]$/) || [])[1] || 0
-            : +(cigar.match(/^(\d+)([SH])/) || [])[1] || 0;
+        return getClip(cigar, this.get('strand'));
     }
 }
 //# sourceMappingURL=BamSlightlyLazyFeature.js.map

package/esm/BamAdapter/BamSlightlyLazyFeature.js.map

@@ -1 +1 @@
-{"version":3,"file":"BamSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/BamAdapter/BamSlightlyLazyFeature.ts"],"names":[],"mappings":"AAOA,SAAS;AACT,OAAO,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAA;AAGhD,MAAM,CAAC,OAAO,OAAO,sBAAsB;IACzC,wEAAwE;IACxE,iFAAiF;IACjF,YACU,MAAiB,EACjB,OAAmB,EACnB,GAAY;QAFZ,WAAM,GAAN,MAAM,CAAW;QACjB,YAAO,GAAP,OAAO,CAAY;QACnB,QAAG,GAAH,GAAG,CAAS;IACnB,CAAC;IAEJ,SAAS;QACP,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,CAAC;IAED,SAAS;QACP,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;IAC9B,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAA;IAC1B,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,qBAAqB;QACnB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,CAAC;IAED,gBAAgB;QACd,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAA;IAClC,CAAC;IAED,WAAW;QACT,aAAa;QACb,OAAO,IAAI,CAAC,MAAM,CAAC,MAAM,CAAA;IAC3B,CAAC;IAED,iBAAiB;QACf,OAAO,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,CAAA;IAC5D,CAAC;IAED,0BAA0B;QACxB,MAAM,EAAE,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,CAAA;QAChC,OAAO,MAAM,CAAC,QAAQ,EAAE;YACtB,CAAC,CAAC,GAAG,OAAO,CAAC,WAAW,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,IAAI,MAAM,CAAC,SAAS,EAAE,GAAG,CAAC,EAAE;YAC1E,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAA;IACnC,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE,CAAA;IAC9B,CAAC;IAED,GAAG,KAAI,CAAC;IAER,IAAI;QACF,MAAM,UAAU,GAAG,MAAM,CAAC,mBAAmB,CAC3C,sBAAsB,CAAC,SAAS,CACjC,CAAA;QAED,OAAO;YACL,GAAG,IAAI,GAAG,CACR,UAAU;iBACP,MAAM,CACL,IAAI,CAAC,EAAE,CACL,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC;gBACxB,IAAI,KAAK,iBAAiB;gBAC1B,IAAI,KAAK,WAAW;gBACpB,IAAI,KAAK,kBAAkB;gBAC3B,IAAI,KAAK,aAAa,CACzB;iBACA,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC;iBAClD,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,EAAE,CAAC,CAC/B;SACF,CAAA;IACH,CAAC;IAED,EAAE;QACA,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,EAAE,CAAA;IACjD,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,KAAa;QACf,MAAM,UAAU,GAAG,QAAQ,KAAK,EAAE,CAAA;QAClC,aAAa;QACb,IAAI,IAAI,CAAC,UAAU,CAAC,EAAE;YACpB,aAAa;YACb,OAAO,IAAI,CAAC,UAAU,CAAC,EAAE,CAAA;SAC1B;QACD,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC/B,CAAC;IAED,YAAY;QACV,OAAO,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,CAAA;IACvD,CAAC;IAED,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,aAAa;QACX,OAAO,KAAK,CAAA;IACd,CAAC;IAED,MAAM;QACJ,OAAO;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI,CAAC,IAAI,EAAE;iBACR,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;iBAC1B,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CACvC;YACD,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE;SACpB,CAAA;IACH,CAAC;IAED,eAAe;QACb,OAAO,aAAa,CAClB,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,EACjB,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,EACd,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,EACf,IAAI,CAAC,GAAG,EACR,IAAI,CAAC,OAAO,EAAE,CACf,CAAA;IACH,CAAC;IAED,YAAY;QACV,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,EAAE,CAAA;QACrC,OAAO,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;YAC9B,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,YAAY,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;YAC5C,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,cAAc,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IAClD,CAAC;CACF"}
+{"version":3,"file":"BamSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/BamAdapter/BamSlightlyLazyFeature.ts"],"names":[],"mappings":"AAOA,SAAS;AACT,OAAO,EAAE,OAAO,EAAE,aAAa,EAAE,MAAM,mBAAmB,CAAA;AAG1D,MAAM,CAAC,OAAO,OAAO,sBAAsB;IACzC,wEAAwE;IACxE,iFAAiF;IACjF,YACU,MAAiB,EACjB,OAAmB,EACnB,GAAY;QAFZ,WAAM,GAAN,MAAM,CAAW;QACjB,YAAO,GAAP,OAAO,CAAY;QACnB,QAAG,GAAH,GAAG,CAAS;IACnB,CAAC;IAEJ,SAAS;QACP,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,CAAC;IAED,SAAS;QACP,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;IAC9B,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAA;IAC1B,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,qBAAqB;QACnB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE;YAC3B,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC;YACrD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IACrE,CAAC;IAED,0BAA0B;QACxB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE;YAC3B,CAAC,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,IACpD,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,GAAG,CAC5B,EAAE;YACJ,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAA;IACnC,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE,CAAA;IAC9B,CAAC;IAED,GAAG,KAAI,CAAC;IAER,IAAI;QACF,MAAM,UAAU,GAAG,MAAM,CAAC,mBAAmB,CAC3C,sBAAsB,CAAC,SAAS,CACjC,CAAA;QAED,OAAO;YACL,GAAG,IAAI,GAAG,CACR,UAAU;iBACP,MAAM,CACL,IAAI,CAAC,EAAE,CACL,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC;gBACxB,IAAI,KAAK,iBAAiB;gBAC1B,IAAI,KAAK,WAAW,CACvB;iBACA,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC;iBAClD,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,EAAE,CAAC,CAC/B;SACF,CAAA;IACH,CAAC;IAED,EAAE;QACA,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,EAAE,CAAA;IACjD,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,KAAa;QACf,MAAM,UAAU,GAAG,QAAQ,KAAK,EAAE,CAAA;QAClC,aAAa;QACb,IAAI,IAAI,CAAC,UAAU,CAAC,EAAE;YACpB,aAAa;YACb,OAAO,IAAI,CAAC,UAAU,CAAC,EAAE,CAAA;SAC1B;QACD,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC/B,CAAC;IAED,YAAY;QACV,OAAO,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,CAAA;IACvD,CAAC;IAED,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,aAAa;QACX,OAAO,KAAK,CAAA;IACd,CAAC;IAED,MAAM;QACJ,OAAO;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI,CAAC,IAAI,EAAE;iBACR,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;iBAC1B,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CACvC;YACD,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE;SACpB,CAAA;IACH,CAAC;IAED,eAAe;QACb,OAAO,aAAa,CAClB,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,EACjB,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,EACd,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,EACf,IAAI,CAAC,GAAG,EACR,IAAI,CAAC,OAAO,EAAE,CACf,CAAA;IACH,CAAC;IAED,YAAY;QACV,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,EAAE,CAAA;QACrC,OAAO,OAAO,CAAC,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAA;IAC3C,CAAC;CACF"}

package/esm/BamAdapter/index.js

@@ -4,6 +4,7 @@ export default (pluginManager) => {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
             name: 'BamAdapter',
+            displayName: 'BAM adapter',
             configSchema,
             getAdapterClass: () => import('./BamAdapter').then(r => r.default),
         });

package/esm/BamAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BamAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,YAAY;YAClB,YAAY;YACZ,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,cAAc,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACnE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BamAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,YAAY;YAClB,WAAW,EAAE,aAAa;YAC1B,YAAY;YACZ,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,cAAc,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACnE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/esm/CramAdapter/CramSlightlyLazyFeature.d.ts

@@ -1,7 +1,6 @@
 import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
 import { CramRecord } from '@gmod/cram';
 import CramAdapter from './CramAdapter';
-import { Mismatch } from './util';
 export default class CramSlightlyLazyFeature implements Feature {
     private record;
     private _store;
@@ -17,25 +16,24 @@ export default class CramSlightlyLazyFeature implements Feature {
     _read_group_id(): string | undefined;
     _get_qual(): string;
     qualRaw(): number[] | null | undefined;
-    _get_seq_id(): string | undefined;
     _get_refName(): string | undefined;
     _get_is_paired(): boolean;
     _get_pair_orientation(): string | null | undefined;
     _get_template_length(): number | undefined;
-    _get_next_seq_id(): string | undefined;
-    _get_next_pos(): number | undefined;
+    _get_next_ref(): string | undefined;
     _get_next_segment_position(): string | undefined;
+    _get_next_pos(): number | undefined;
     _get_tags(): Record<string, string>;
     _get_seq(): string | null | undefined;
     _get_CIGAR(): string;
     tags(): string[];
     id(): string;
     get(field: string): any;
-    parent(): undefined | Feature;
-    children(): undefined | Feature[];
+    parent(): undefined;
+    children(): undefined;
     set(): void;
     pairedFeature(): boolean;
     _get_clipPos(): any;
     toJSON(): SimpleFeatureSerialized;
-    _get_mismatches(): Mismatch[];
+    _get_mismatches(): import("./util").Mismatch[];
 }

package/esm/CramAdapter/CramSlightlyLazyFeature.js

@@ -41,11 +41,8 @@ export default class CramSlightlyLazyFeature {
     qualRaw() {
         return this.record.qualityScores;
     }
-    _get_seq_id() {
-        return this._store.refIdToName(this.record.sequenceId);
-    }
     _get_refName() {
-        return this._get_seq_id();
+        return this._store.refIdToName(this.record.sequenceId);
     }
     _get_is_paired() {
         return !!this.record.mate;
@@ -56,19 +53,20 @@ export default class CramSlightlyLazyFeature {
     _get_template_length() {
         return this.record.templateLength || this.record.templateSize;
     }
-    _get_next_seq_id() {
+    _get_next_ref() {
         return this.record.mate
             ? this._store.refIdToName(this.record.mate.sequenceId)
             : undefined;
     }
-    _get_next_pos() {
-        return this.record.mate ? this.record.mate.alignmentStart : undefined;
-    }
     _get_next_segment_position() {
         return this.record.mate
             ? `${this._store.refIdToName(this.record.mate.sequenceId)}:${this.record.mate.alignmentStart}`
             : undefined;
     }
+    _get_next_pos() {
+        var _a;
+        return (_a = this.record.mate) === null || _a === void 0 ? void 0 : _a.alignmentStart;
+    }
     _get_tags() {
         const RG = this._read_group_id();
         const { tags } = this.record;

package/esm/CramAdapter/CramSlightlyLazyFeature.js.map

@@ -1 +1 @@
-{"version":3,"file":"CramSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/CramAdapter/CramSlightlyLazyFeature.ts"],"names":[],"mappings":"AAOA,OAAO,EAAY,mBAAmB,EAAE,wBAAwB,EAAE,MAAM,QAAQ,CAAA;AAEhF,MAAM,CAAC,OAAO,OAAO,uBAAuB;IAC1C,wEAAwE;IACxE,iFAAiF;IACjF,YAAoB,MAAkB,EAAU,MAAmB;QAA/C,WAAM,GAAN,MAAM,CAAY;QAAU,WAAM,GAAN,MAAM,CAAa;IAAG,CAAC;IAEvE,SAAS;QACP,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAA;IAC7B,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,GAAG,CAAC,CAAA;IACvC,CAAC;IAED,QAAQ;;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,GAAG,CAAC,MAAA,IAAI,CAAC,MAAM,CAAC,WAAW,mCAAI,CAAC,CAAC,GAAG,CAAC,CAAA;IACxE,CAAC;IAED,uBAAuB;QACrB,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;IACjC,CAAC;IAED,SAAS;QACP,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,CAAA;IACnC,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAA;IAC1B,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,cAAc;QACZ,MAAM,EAAE,GAAG,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC,UAAU,CAAA;QAC3C,OAAO,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACrD,CAAC;IAED,SAAS;QACP,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,aAAa,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACpD,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,aAAa,CAAA;IAClC,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IACxD,CAAC;IAED,YAAY;QACV,OAAO,IAAI,CAAC,WAAW,EAAE,CAAA;IAC3B,CAAC;IAED,cAAc;QACZ,OAAO,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAA;IAC3B,CAAC;IAED,qBAAqB;QACnB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,CAAC;IAED,oBAAoB;QAClB,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,IAAI,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;IAC/D,CAAC;IAED,gBAAgB;QACd,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI;YACrB,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC;YACtD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,SAAS,CAAA;IACvE,CAAC;IAED,0BAA0B;QACxB,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI;YACrB,CAAC,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC,IACrD,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,cACnB,EAAE;YACJ,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,SAAS;QACP,MAAM,EAAE,GAAG,IAAI,CAAC,cAAc,EAAE,CAAA;QAChC,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAC,MAAM,CAAA;QAC5B,4DAA4D;QAC5D,OAAO,EAAE,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,GAAG,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAA;IAClD,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAA;IACnC,CAAC;IAED,kDAAkD;IAClD,UAAU;QACR,OAAO,mBAAmB,CACxB,IAAI,CAAC,MAAM,CAAC,YAAY,EACxB,IAAI,CAAC,MAAM,CAAC,cAAc,EAC1B,IAAI,CAAC,MAAM,CAAC,UAAU,EACtB,IAAI,CAAC,MAAM,CAAC,UAAU,CACvB,CAAA;IACH,CAAC;IAED,IAAI;QACF,OAAO,MAAM,CAAC,mBAAmB,CAAC,uBAAuB,CAAC,SAAS,CAAC;aACjE,MAAM,CACL,IAAI,CAAC,EAAE,CACL,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC;YACxB,IAAI,KAAK,iBAAiB;YAC1B,IAAI,KAAK,yBAAyB,CACrC;aACA,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAA;IACvD,CAAC;IAED,EAAE;QACA,OAAO,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAA;IACpD,CAAC;IAED,GAAG,CAAC,KAAa;QACf,MAAM,UAAU,GAAG,QAAQ,KAAK,EAAE,CAAA;QAClC,aAAa;QACb,IAAI,IAAI,CAAC,UAAU,CAAC,EAAE;YACpB,aAAa;YACb,OAAO,IAAI,CAAC,UAAU,CAAC,EAAE,CAAA;SAC1B;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,GAAG,KAAU,CAAC;IAEd,aAAa;QACX,OAAO,KAAK,CAAA;IACd,CAAC;IAED,YAAY;QACV,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;QACzC,IAAI,UAAU,CAAC,MAAM,EAAE;YACrB,MAAM,MAAM,GACV,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;gBACvB,CAAC,CAAC,UAAU,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC,CAAC;gBACnC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;YACnB,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;YAChC,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,UAAU,EAAE;gBAC9C,OAAO,OAAO,CAAA;aACf;SACF;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,MAAM;QACJ,OAAO;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI,CAAC,IAAI,EAAE;iBACR,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;iBAC1B,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CACvC;YACD,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE;SACpB,CAAA;IACH,CAAC;IAED,eAAe;QACb,MAAM,YAAY,GAAG,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;QAC7C,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,EAAE,CAAA;QAC3B,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QAC/B,OAAO,wBAAwB,CAAC,YAAY,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;IAC5D,CAAC;CACF"}
+{"version":3,"file":"CramSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/CramAdapter/CramSlightlyLazyFeature.ts"],"names":[],"mappings":"AASA,OAAO,EAAE,mBAAmB,EAAE,wBAAwB,EAAE,MAAM,QAAQ,CAAA;AAEtE,MAAM,CAAC,OAAO,OAAO,uBAAuB;IAC1C,wEAAwE;IACxE,iFAAiF;IACjF,YAAoB,MAAkB,EAAU,MAAmB;QAA/C,WAAM,GAAN,MAAM,CAAY;QAAU,WAAM,GAAN,MAAM,CAAa;IAAG,CAAC;IAEvE,SAAS;QACP,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAA;IAC7B,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,GAAG,CAAC,CAAA;IACvC,CAAC;IAED,QAAQ;;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,GAAG,CAAC,MAAA,IAAI,CAAC,MAAM,CAAC,WAAW,mCAAI,CAAC,CAAC,GAAG,CAAC,CAAA;IACxE,CAAC;IAED,uBAAuB;QACrB,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;IACjC,CAAC;IAED,SAAS;QACP,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,CAAA;IACnC,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAA;IAC1B,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,cAAc;QACZ,MAAM,EAAE,GAAG,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC,UAAU,CAAA;QAC3C,OAAO,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACrD,CAAC;IAED,SAAS;QACP,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,aAAa,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACpD,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,aAAa,CAAA;IAClC,CAAC;IAED,YAAY;QACV,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IACxD,CAAC;IAED,cAAc;QACZ,OAAO,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAA;IAC3B,CAAC;IAED,qBAAqB;QACnB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,CAAC;IAED,oBAAoB;QAClB,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,IAAI,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;IAC/D,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI;YACrB,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC;YACtD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,0BAA0B;QACxB,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI;YACrB,CAAC,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC,IACrD,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,cACnB,EAAE;YACJ,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,aAAa;;QACX,OAAO,MAAA,IAAI,CAAC,MAAM,CAAC,IAAI,0CAAE,cAAc,CAAA;IACzC,CAAC;IAED,SAAS;QACP,MAAM,EAAE,GAAG,IAAI,CAAC,cAAc,EAAE,CAAA;QAChC,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAC,MAAM,CAAA;QAC5B,4DAA4D;QAC5D,OAAO,EAAE,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,GAAG,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAA;IAClD,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAA;IACnC,CAAC;IAED,kDAAkD;IAClD,UAAU;QACR,OAAO,mBAAmB,CACxB,IAAI,CAAC,MAAM,CAAC,YAAY,EACxB,IAAI,CAAC,MAAM,CAAC,cAAc,EAC1B,IAAI,CAAC,MAAM,CAAC,UAAU,EACtB,IAAI,CAAC,MAAM,CAAC,UAAU,CACvB,CAAA;IACH,CAAC;IAED,IAAI;QACF,OAAO,MAAM,CAAC,mBAAmB,CAAC,uBAAuB,CAAC,SAAS,CAAC;aACjE,MAAM,CACL,IAAI,CAAC,EAAE,CACL,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC;YACxB,IAAI,KAAK,iBAAiB;YAC1B,IAAI,KAAK,yBAAyB,CACrC;aACA,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAA;IACvD,CAAC;IAED,EAAE;QACA,OAAO,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAA;IACpD,CAAC;IAED,GAAG,CAAC,KAAa;QACf,MAAM,UAAU,GAAG,QAAQ,KAAK,EAAE,CAAA;QAClC,aAAa;QACb,IAAI,IAAI,CAAC,UAAU,CAAC,EAAE;YACpB,aAAa;YACb,OAAO,IAAI,CAAC,UAAU,CAAC,EAAE,CAAA;SAC1B;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,GAAG,KAAI,CAAC;IAER,aAAa;QACX,OAAO,KAAK,CAAA;IACd,CAAC;IAED,YAAY;QACV,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;QACzC,IAAI,UAAU,CAAC,MAAM,EAAE;YACrB,MAAM,MAAM,GACV,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;gBACvB,CAAC,CAAC,UAAU,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC,CAAC;gBACnC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;YACnB,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;YAChC,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,UAAU,EAAE;gBAC9C,OAAO,OAAO,CAAA;aACf;SACF;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,MAAM;QACJ,OAAO;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI,CAAC,IAAI,EAAE;iBACR,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;iBAC1B,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CACvC;YACD,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE;SACpB,CAAA;IACH,CAAC;IAED,eAAe;QACb,MAAM,YAAY,GAAG,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;QAC7C,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,EAAE,CAAA;QAC3B,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QAC/B,OAAO,wBAAwB,CAAC,YAAY,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;IAC5D,CAAC;CACF"}

package/esm/CramAdapter/index.js

@@ -5,6 +5,7 @@ export default (pluginManager) => {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
             name: 'CramAdapter',
+            displayName: 'CRAM adapter',
             configSchema,
             getAdapterClass: () => import('./CramAdapter').then(r => r.default),
         });

package/esm/CramAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/CramAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,SAAS;AACT,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,aAAa;YACnB,YAAY;YACZ,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,eAAe,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACpE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/CramAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,SAAS;AACT,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,aAAa;YACnB,WAAW,EAAE,cAAc;YAC3B,YAAY;YACZ,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,eAAe,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACpE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/esm/GuessAlignmentsTypes/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/GuessAlignmentsTypes/index.js

@@ -0,0 +1,54 @@
+import { makeIndex, makeIndexType, getFileName, } from '@jbrowse/core/util/tracks';
+export default (pluginManager) => {
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const regexGuess = /\.cram$/i;
+            const adapterName = 'CramAdapter';
+            const fileName = getFileName(file);
+            const obj = {
+                type: adapterName,
+                cramLocation: file,
+                craiLocation: index || makeIndex(file, '.crai'),
+            };
+            if (regexGuess.test(fileName) && !adapterHint) {
+                return obj;
+            }
+            else if (adapterHint === adapterName) {
+                return obj;
+            }
+            return adapterGuesser(file, index, adapterHint);
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const regexGuess = /\.bam$/i;
+            const adapterName = 'BamAdapter';
+            const fileName = getFileName(file);
+            const indexName = index && getFileName(index);
+            const obj = {
+                type: adapterName,
+                bamLocation: file,
+                index: {
+                    location: index || makeIndex(file, '.bai'),
+                    indexType: makeIndexType(indexName, 'CSI', 'BAI'),
+                },
+            };
+            if (regexGuess.test(fileName) && !adapterHint) {
+                return obj;
+            }
+            else if (adapterHint === adapterName) {
+                return obj;
+            }
+            return adapterGuesser(file, index, adapterHint);
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+        return (adapterName) => {
+            if (adapterName === 'BamAdapter' || adapterName === 'CramAdapter') {
+                return 'AlignmentsTrack';
+            }
+            return trackTypeGuesser(adapterName);
+        };
+    });
+};
+//# sourceMappingURL=index.js.map

package/esm/GuessAlignmentsTypes/index.js.map

@@ -0,0 +1 @@
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package/esm/HtsgetBamAdapter/index.js

@@ -1,16 +1,16 @@
 import configSchema from './configSchema';
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 export default (pluginManager) => {
-    pluginManager.addAdapterType(() => new AdapterType({
-        name: 'HtsgetBamAdapter',
-        adapterMetadata: {
-            category: null,
-            hiddenFromGUI: true,
-            displayName: null,
-            description: null,
-        },
-        configSchema,
-        getAdapterClass: () => import('./HtsgetBamAdapter').then(r => r.default),
-    }));
+    pluginManager.addAdapterType(() => {
+        return new AdapterType({
+            name: 'HtsgetBamAdapter',
+            displayName: 'Htsget BAM adapter',
+            adapterMetadata: {
+                hiddenFromGUI: true,
+            },
+            configSchema,
+            getAdapterClass: () => import('./HtsgetBamAdapter').then(r => r.default),
+        });
+    });
 };
 //# sourceMappingURL=index.js.map

package/esm/HtsgetBamAdapter/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,kBAAkB;YACxB,WAAW,EAAE,oBAAoB;YACjC,eAAe,EAAE;gBACf,aAAa,EAAE,IAAI;aACpB;YACD,YAAY;YACZ,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,oBAAoB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACzE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js

@@ -11,24 +11,21 @@ const useStyles = makeStyles()(() => ({
     },
 }));
 function AlignmentsDisplay({ model }) {
-    const { PileupDisplay, SNPCoverageDisplay, showPileup, showCoverage } = model;
+    const { PileupDisplay, SNPCoverageDisplay } = model;
     const { classes } = useStyles();
     const top = SNPCoverageDisplay.height;
     return (React.createElement("div", { "data-testid": `display-${getConf(model, 'displayId')}`, style: { position: 'relative' } },
-        showCoverage ? (React.createElement(React.Fragment, null,
-            React.createElement("div", { "data-testid": "Blockset-snpcoverage" },
-                React.createElement(SNPCoverageDisplay.RenderingComponent, { model: SNPCoverageDisplay })),
-            React.createElement(ResizeHandle, { onDrag: delta => {
-                    SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta);
-                    return delta;
-                }, className: classes.resizeHandle, style: {
-                    top,
-                } }))) : null,
-        showPileup ? (React.createElement("div", { "data-testid": "Blockset-pileup", style: {
+        React.createElement("div", { "data-testid": "Blockset-snpcoverage" },
+            React.createElement(SNPCoverageDisplay.RenderingComponent, { model: SNPCoverageDisplay })),
+        React.createElement(ResizeHandle, { onDrag: delta => {
+                SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta);
+                return delta;
+            }, className: classes.resizeHandle, style: { top } }),
+        React.createElement("div", { "data-testid": "Blockset-pileup", style: {
                 position: 'absolute',
-                top: showCoverage ? SNPCoverageDisplay.height : 0,
+                top,
             } },
-            React.createElement(PileupDisplay.RenderingComponent, { model: PileupDisplay }))) : null));
+            React.createElement(PileupDisplay.RenderingComponent, { model: PileupDisplay }))));
 }
 export default observer(AlignmentsDisplay);
 //# sourceMappingURL=AlignmentsDisplay.js.map

package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map

@@ -1 +1 @@
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package/esm/LinearAlignmentsDisplay/index.js

@@ -8,6 +8,7 @@ export default function (pluginManager) {
         const configSchema = configSchemaFactory(pluginManager);
         return new DisplayType({
             name: 'LinearAlignmentsDisplay',
+            displayName: 'Alignments display (combination)',
             configSchema,
             stateModel: modelFactory(pluginManager, configSchema),
             trackType: 'AlignmentsTrack',

package/esm/LinearAlignmentsDisplay/index.js.map

@@ -1 +1 @@
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package/esm/LinearAlignmentsDisplay/models/configSchema.d.ts

@@ -1,4 +1,7 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const configModelFactory: (pm: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export type AlignmentsConfigModel = ReturnType<typeof configModelFactory>;
-export default configModelFactory;
+/**
+ * #config LinearAlignmentsDisplay
+ * has a "pileup" sub-display, where you can see individual reads and a
+ * quantitative "snpcoverage" sub-display track showing SNP frequencies
+ */
+export default function configModelFactory(pm: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/esm/LinearAlignmentsDisplay/models/configSchema.js

@@ -5,8 +5,7 @@ import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-vie
  * has a "pileup" sub-display, where you can see individual reads and a
  * quantitative "snpcoverage" sub-display track showing SNP frequencies
  */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
-const configModelFactory = (pm) => {
+export default function configModelFactory(pm) {
     return ConfigurationSchema('LinearAlignmentsDisplay', {
         /**
          * #slot
@@ -24,6 +23,5 @@ const configModelFactory = (pm) => {
         baseConfiguration: baseLinearDisplayConfigSchema,
         explicitlyTyped: true,
     });
-};
-export default configModelFactory;
+}
 //# sourceMappingURL=configSchema.js.map

package/esm/LinearAlignmentsDisplay/models/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/models/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,6BAA6B,EAAE,MAAM,oCAAoC,CAAA;AAGlF;;;;GAIG;AACH,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,EAAiB;IAC1D,OAAO,mBAAmB,CACxB,yBAAyB,EACzB;QACE;;WAEG;QACH,aAAa,EAAE,EAAE,CAAC,cAAc,CAAC,qBAAqB,CAAC,CAAC,YAAY;QAEpE;;WAEG;QACH,kBAAkB,EAAE,EAAE,CAAC,cAAc,CAAC,0BAA0B,CAAC;aAC9D,YAAY;KAChB,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,6BAA6B;QAChD,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC"}