@jbrowse/plugin-alignments 2.2.1 → 2.3.0

package/esm/{LinearPileupDisplay/components → shared}/FilterByTag.js

@@ -1,19 +1,13 @@
 import React, { useState } from 'react';
 import { observer } from 'mobx-react';
-import { Button, Dialog, DialogActions, DialogContent, DialogTitle, IconButton, Link, Paper, TextField, Typography, } from '@mui/material';
+import { Button, DialogActions, DialogContent, Link, Paper, TextField, Typography, } from '@mui/material';
+import { Dialog } from '@jbrowse/core/ui';
 import { makeStyles } from 'tss-react/mui';
-import CloseIcon from '@mui/icons-material/Close';
 const useStyles = makeStyles()(theme => ({
     paper: {
         padding: theme.spacing(2),
         margin: theme.spacing(2),
     },
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
     field: {
         margin: theme.spacing(2),
     },
@@ -63,11 +57,7 @@ function FilterByTagDlg(props) {
     const [readName, setReadName] = useState((filterBy === null || filterBy === void 0 ? void 0 : filterBy.readName) || '');
     const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
     const site = 'https://broadinstitute.github.io/picard/explain-flags.html';
-    return (React.createElement(Dialog, { open: true, onClose: handleClose },
-        React.createElement(DialogTitle, null,
-            "Filter options",
-            React.createElement(IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose },
-                React.createElement(CloseIcon, null))),
+    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Filter options" },
         React.createElement(DialogContent, null,
             React.createElement(Typography, null,
                 "Set filter bitmask options. Refer to ",
@@ -84,22 +74,16 @@ function FilterByTagDlg(props) {
                         React.createElement(Bitmask, { flag: flagExclude, setFlag: setFlagExclude })))),
             React.createElement(Paper, { className: classes.paper, variant: "outlined" },
                 React.createElement(Typography, null, "Filter by tag name and value. Use * in the value field to get all reads containing any value for that tag. Example: filter tag name SA with value * to get all split/supplementary reads. Other examples include HP for haplotype, or RG for read group"),
-                React.createElement(TextField, { className: classes.field, value: tag, onChange: event => {
-                        setTag(event.target.value);
-                    }, placeholder: "Enter tag name", inputProps: {
+                React.createElement(TextField, { className: classes.field, value: tag, onChange: event => setTag(event.target.value), placeholder: "Enter tag name", inputProps: {
                         maxLength: 2,
                         'data-testid': 'color-tag-name-input',
                     }, error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', "data-testid": "color-tag-name" }),
-                React.createElement(TextField, { className: classes.field, value: tagValue, onChange: event => {
-                        setTagValue(event.target.value);
-                    }, placeholder: "Enter tag value", inputProps: {
+                React.createElement(TextField, { className: classes.field, value: tagValue, onChange: event => setTagValue(event.target.value), placeholder: "Enter tag value", inputProps: {
                         'data-testid': 'color-tag-name-input',
                     }, "data-testid": "color-tag-value" })),
             React.createElement(Paper, { className: classes.paper, variant: "outlined" },
                 React.createElement(Typography, null, "Filter by read name"),
-                React.createElement(TextField, { className: classes.field, value: readName, onChange: event => {
-                        setReadName(event.target.value);
-                    }, placeholder: "Enter read name", inputProps: {
+                React.createElement(TextField, { className: classes.field, value: readName, onChange: event => setReadName(event.target.value), placeholder: "Enter read name", inputProps: {
                         'data-testid': 'color-tag-readname-input',
                     }, "data-testid": "color-tag-readname" })),
             React.createElement(DialogActions, null,

package/esm/shared/FilterByTag.js.map

@@ -0,0 +1 @@
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package/esm/shared/color.d.ts

@@ -0,0 +1,17 @@
+import { ChainStats } from './fetchChains';
+export declare function getInsertSizeColor(f1: {
+    refName: string;
+    tlen?: number;
+}, f2: {
+    refName: string;
+}, stats?: ChainStats): "" | "red" | "purple" | "#f0f";
+export declare function getInsertSizeAndOrientationColor(f1: {
+    refName: string;
+    pair_orientation?: string;
+    tlen?: number;
+}, f2: {
+    refName: string;
+}, stats?: ChainStats): string;
+export declare function getOrientationColor(f: {
+    pair_orientation?: string;
+}): string;

package/esm/shared/color.js

@@ -0,0 +1,37 @@
+import { orientationTypes } from '../util';
+const alignmentColoring = {
+    color_pair_lr: '#c8c8c8',
+    color_pair_rr: 'navy',
+    color_pair_rl: 'teal',
+    color_pair_ll: 'green',
+};
+export function getInsertSizeColor(f1, f2, stats) {
+    const sameRef = f1.refName === f2.refName;
+    const tlen = Math.abs(f1.tlen || 0);
+    if (sameRef && tlen > ((stats === null || stats === void 0 ? void 0 : stats.upper) || 0)) {
+        return 'red';
+    }
+    else if (sameRef && tlen < ((stats === null || stats === void 0 ? void 0 : stats.lower) || 0)) {
+        return '#f0f';
+    }
+    else if (!sameRef) {
+        return 'purple';
+    }
+    return '';
+}
+export function getInsertSizeAndOrientationColor(f1, f2, stats) {
+    return getInsertSizeColor(f1, f2, stats) || getOrientationColor(f1);
+}
+export function getOrientationColor(f) {
+    const type = orientationTypes['fr'];
+    const orientation = type[f.pair_orientation || ''];
+    const map = {
+        LR: 'color_pair_lr',
+        RR: 'color_pair_rr',
+        RL: 'color_pair_rl',
+        LL: 'color_pair_ll',
+    };
+    const val = map[orientation];
+    return alignmentColoring[val] || 'grey';
+}
+//# sourceMappingURL=color.js.map

package/esm/shared/color.js.map

@@ -0,0 +1 @@
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package/esm/shared/fetchChains.d.ts

@@ -0,0 +1,27 @@
+import { IAnyStateTreeNode } from 'mobx-state-tree';
+export interface ReducedFeature {
+    name: string;
+    strand: number;
+    refName: string;
+    start: number;
+    end: number;
+    id: string;
+    flags: number;
+    tlen: number;
+    pair_orientation: string;
+    next_ref?: string;
+    next_pos?: number;
+    clipPos: number;
+    SA?: string;
+}
+export interface ChainStats {
+    max: number;
+    min: number;
+    upper: number;
+    lower: number;
+}
+export interface ChainData {
+    chains: ReducedFeature[][];
+    stats?: ChainStats;
+}
+export declare function fetchChains(self: IAnyStateTreeNode): Promise<void>;

package/esm/shared/fetchChains.js

@@ -0,0 +1,26 @@
+import { getContainingTrack, getContainingView, getSession, } from '@jbrowse/core/util';
+import { getSnapshot } from 'mobx-state-tree';
+export async function fetchChains(self) {
+    try {
+        const { rpcSessionId: sessionId } = getContainingTrack(self);
+        const { rpcManager } = getSession(self);
+        const view = getContainingView(self);
+        if (!view.initialized || self.error) {
+            return;
+        }
+        self.setLoading(true);
+        const ret = (await rpcManager.call(sessionId, 'PileupGetReducedFeatures', {
+            sessionId,
+            regions: view.staticBlocks.contentBlocks,
+            filterBy: getSnapshot(self.filterBy),
+            adapterConfig: self.adapterConfig,
+        }));
+        self.setChainData(ret);
+        self.setLoading(false);
+    }
+    catch (e) {
+        console.error(e);
+        self.setError(e);
+    }
+}
+//# sourceMappingURL=fetchChains.js.map

package/esm/shared/fetchChains.js.map

@@ -0,0 +1 @@
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package/esm/shared/index.d.ts

@@ -0,0 +1,36 @@
+import { IAnyStateTreeNode } from 'mobx-state-tree';
+import { BlockSet } from '@jbrowse/core/util/blockTypes';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export declare function getUniqueTagValues(self: IAnyStateTreeNode & {
+    adapterConfig: AnyConfigurationModel;
+}, colorScheme: {
+    type: string;
+    tag?: string;
+}, blocks: BlockSet, opts?: {
+    headers?: Record<string, string>;
+    signal?: AbortSignal;
+    filters?: string[];
+}): Promise<string[]>;
+type Track = IAnyStateTreeNode & {
+    configuration: AnyConfigurationModel;
+};
+export declare function getUniqueModificationValues(self: IAnyStateTreeNode & {
+    parentTrack: Track;
+}, adapterConfig: AnyConfigurationModel, colorScheme: {
+    type: string;
+    tag?: string;
+}, blocks: BlockSet, opts?: {
+    headers?: Record<string, string>;
+    signal?: AbortSignal;
+    filters?: string[];
+}): Promise<string[]>;
+export declare const FilterModel: import("mobx-state-tree").IModelType<{
+    flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    flagExclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    tagFilter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+        tag: import("mobx-state-tree").ISimpleType<string>;
+        value: import("mobx-state-tree").ISimpleType<string>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export {};

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

@@ -1,3 +1,4 @@
+import { types } from 'mobx-state-tree';
 import { getSession } from '@jbrowse/core/util';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
 export async function getUniqueTagValues(self, colorScheme, blocks, opts) {
@@ -25,4 +26,13 @@ export async function getUniqueModificationValues(self, adapterConfig, colorSche
     });
     return values;
 }
-//# sourceMappingURL=shared.js.map
+export const FilterModel = types.model({
+    flagInclude: types.optional(types.number, 0),
+    flagExclude: types.optional(types.number, 1540),
+    readName: types.maybe(types.string),
+    tagFilter: types.maybe(types.model({
+        tag: types.string,
+        value: types.string,
+    })),
+});
+//# sourceMappingURL=index.js.map

package/esm/shared/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/shared/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAqB,MAAM,iBAAiB,CAAA;AAE1D,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAA;AAG3D,MAAM,CAAC,KAAK,UAAU,kBAAkB,CACtC,IAAkE,EAClE,WAA2C,EAC3C,MAAgB,EAChB,IAIC;IAED,MAAM,EAAE,UAAU,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;IACvC,MAAM,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;IAC9B,MAAM,SAAS,GAAG,eAAe,CAAC,IAAI,CAAC,CAAA;IACvC,MAAM,MAAM,GAAG,MAAM,UAAU,CAAC,IAAI,CAClC,eAAe,CAAC,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;AAID,MAAM,CAAC,KAAK,UAAU,2BAA2B,CAC/C,IAEC,EACD,aAAoC,EACpC,WAA2C,EAC3C,MAAgB,EAChB,IAIC;IAED,MAAM,EAAE,UAAU,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;IACvC,MAAM,SAAS,GAAG,eAAe,CAAC,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;AAED,MAAM,CAAC,MAAM,WAAW,GAAG,KAAK,CAAC,KAAK,CAAC;IACrC,WAAW,EAAE,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC;IAC5C,WAAW,EAAE,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC;IAC/C,QAAQ,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;IACnC,SAAS,EAAE,KAAK,CAAC,KAAK,CACpB,KAAK,CAAC,KAAK,CAAC;QACV,GAAG,EAAE,KAAK,CAAC,MAAM;QACjB,KAAK,EAAE,KAAK,CAAC,MAAM;KACpB,CAAC,CACH;CACF,CAAC,CAAA"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.2.1",
+  "version": "2.3.0",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -27,7 +27,7 @@
     "build": "npm-run-all build:*",
     "test": "cd ../..; jest plugins/alignments",
     "prepublishOnly": "yarn test",
-    "prepack": "yarn build; yarn useDist",
+    "prepack": "yarn build && yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
     "useSrc": "node ../../scripts/useSrc.js",
@@ -40,6 +40,7 @@
     "@gmod/bam": "^1.1.15",
     "@gmod/cram": "^1.7.1",
     "@mui/icons-material": "^5.0.1",
+    "canvas2svg": "^1.0.16",
     "clone": "^2.1.2",
     "color": "^3.1.2",
     "copy-to-clipboard": "^3.3.1",
@@ -54,10 +55,9 @@
     "mobx": "^6.0.0",
     "mobx-react": "^7.0.0",
     "mobx-state-tree": "^5.0.0",
-    "prop-types": "^15.0.0",
     "react": ">=16.8.0",
     "rxjs": "^6.0.0",
-    "tss-react": "^3.0.0"
+    "tss-react": "^4.0.0"
   },
   "publishConfig": {
     "access": "public"
@@ -65,5 +65,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "896d175c5d9345049faea8e1155f243c912aac42"
+  "gitHead": "a85b280a8af4d1a11e81ab42913f5f6049e6e580"
 }

package/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx

@@ -17,7 +17,7 @@ import {
   BaseCard,
   SimpleValue,
 } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'
-import { parseCigar } from '../BamAdapter/MismatchParser'
+import { parseCigar } from '../MismatchParser'
 
 const useStyles = makeStyles()({
   compact: {

package/src/AlignmentsTrack/index.ts

@@ -29,6 +29,7 @@ export default function register(pm: PluginManager) {
     const configSchema = configSchemaFactory(pm)
     const track = new TrackType({
       name: 'AlignmentsTrack',
+      displayName: 'Alignments track',
       configSchema,
       stateModel: createBaseTrackModel(pm, 'AlignmentsTrack', configSchema),
     })

package/src/BamAdapter/BamSlightlyLazyFeature.ts

@@ -6,7 +6,7 @@ import {
 import { BamRecord } from '@gmod/bam'
 
 // locals
-import { getMismatches } from './MismatchParser'
+import { getClip, getMismatches } from '../MismatchParser'
 import BamAdapter from './BamAdapter'
 
 export default class BamSlightlyLazyFeature implements Feature {
@@ -42,23 +42,21 @@ export default class BamSlightlyLazyFeature implements Feature {
     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
   }
 
@@ -84,9 +82,7 @@ export default class BamSlightlyLazyFeature implements Feature {
             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()),
@@ -148,8 +144,6 @@ export default class BamSlightlyLazyFeature implements Feature {
 
   _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'))
   }
 }

package/src/BamAdapter/index.ts

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

package/src/CramAdapter/CramSlightlyLazyFeature.ts

@@ -4,8 +4,10 @@ import {
   SimpleFeatureSerialized,
 } from '@jbrowse/core/util/simpleFeature'
 import { CramRecord } from '@gmod/cram'
+
+// locals
 import CramAdapter from './CramAdapter'
-import { Mismatch, readFeaturesToCIGAR, readFeaturesToMismatches } from './util'
+import { readFeaturesToCIGAR, readFeaturesToMismatches } from './util'
 
 export default class CramSlightlyLazyFeature implements Feature {
   // uses parameter properties to automatically create fields on the class
@@ -57,12 +59,8 @@ export default class CramSlightlyLazyFeature implements Feature {
     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() {
@@ -77,16 +75,12 @@ export default class CramSlightlyLazyFeature implements Feature {
     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
       ? `${this._store.refIdToName(this.record.mate.sequenceId)}:${
@@ -95,6 +89,10 @@ export default class CramSlightlyLazyFeature implements Feature {
       : undefined
   }
 
+  _get_next_pos() {
+    return this.record.mate?.alignmentStart
+  }
+
   _get_tags() {
     const RG = this._read_group_id()
     const { tags } = this.record
@@ -141,15 +139,15 @@ export default class CramSlightlyLazyFeature implements Feature {
     return undefined
   }
 
-  parent(): undefined | Feature {
+  parent() {
     return undefined
   }
 
-  children(): undefined | Feature[] {
+  children() {
     return undefined
   }
 
-  set(): void {}
+  set() {}
 
   pairedFeature() {
     return false
@@ -181,7 +179,7 @@ export default class CramSlightlyLazyFeature implements Feature {
     }
   }
 
-  _get_mismatches(): Mismatch[] {
+  _get_mismatches() {
     const readFeatures = this.record.readFeatures
     const qual = this.qualRaw()
     const start = this.get('start')

package/src/CramAdapter/CramTestAdapters.ts

@@ -89,6 +89,7 @@ export class SequenceAdapter extends BaseFeatureDataAdapter {
           )
           observer.complete()
         })
+        .catch(e => observer.error(e))
       return { unsubscribe: () => {} }
     })
   }

package/src/CramAdapter/__snapshots__/CramAdapter.test.ts.snap

@@ -13,7 +13,6 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
     "refName": "ctgA",
     "score": 37,
     "seq": "TACACTGGTTCGGAGACGGTTCGTGACGAGCGCGCTATATGTCGGCATCTGCGCCGCATGAGCGGCCGCTGACCGGCGGCACGACTAATATAGTGCAAGA",
-    "seq_id": "ctgA",
     "start": 5440,
     "strand": -1,
     "tags": {
@@ -39,7 +38,6 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
     "refName": "ctgA",
     "score": 37,
     "seq": "ACACTGGTTCGGAGACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCGGCCCCTGTCCGGCGGCACGAATAATATAGTGCAAGAA",
-    "seq_id": "ctgA",
     "start": 5441,
     "strand": -1,
     "tags": {
@@ -65,7 +63,6 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
     "refName": "ctgA",
     "score": 37,
     "seq": "CTGGTTCGGAGACGGTTCATGACGACCGCGCTATATGTCGGCATCTGCGTCGCATGAGCGGCCGCTGTCCGGCGGCTCGAATAATATAGTGCAAGAAAAA",
-    "seq_id": "ctgA",
     "start": 5444,
     "strand": 1,
     "tags": {
@@ -91,7 +88,6 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
     "refName": "ctgA",
     "score": 37,
     "seq": "AGACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCGCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACT",
-    "seq_id": "ctgA",
     "start": 5453,
     "strand": 1,
     "tags": {
@@ -117,7 +113,6 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
     "refName": "ctgA",
     "score": 37,
     "seq": "GACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCCGCCGCTGTCCGACGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTA",
-    "seq_id": "ctgA",
     "start": 5454,
     "strand": 1,
     "tags": {
@@ -143,7 +138,6 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
     "refName": "ctgA",
     "score": 37,
     "seq": "TTCATGACGAGCGCGCTATATGACGGCATCTGCGCCGCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTT",
-    "seq_id": "ctgA",
     "start": 5459,
     "strand": -1,
     "tags": {
@@ -169,7 +163,6 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
     "refName": "ctgA",
     "score": 37,
     "seq": "TCATGACGAGCGCGCTATATGTCGGCATCTGCGCCGCATCAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTA",
-    "seq_id": "ctgA",
     "start": 5460,
     "strand": 1,
     "tags": {
@@ -195,7 +188,6 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
     "refName": "ctgA",
     "score": 37,
     "seq": "AGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTATATATGAT",
-    "seq_id": "ctgA",
     "start": 5468,
     "strand": 1,
     "tags": {
@@ -221,7 +213,6 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
     "refName": "ctgA",
     "score": 37,
     "seq": "CCCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCTAAGACTACGGTTATATATGATGGAACGGCCCTCACAGCATTCTCACA",
-    "seq_id": "ctgA",
     "start": 5494,
     "strand": -1,
     "tags": {
@@ -247,7 +238,6 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
     "refName": "ctgA",
     "score": 37,
     "seq": "CATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTATATATGATGGAACGGCCCTCACAGCATTGTAACAGG",
-    "seq_id": "ctgA",
     "start": 5496,
     "strand": 1,
     "tags": {

package/src/CramAdapter/index.ts

@@ -8,6 +8,7 @@ export default (pluginManager: PluginManager) => {
   pluginManager.addAdapterType(() => {
     return new AdapterType({
       name: 'CramAdapter',
+      displayName: 'CRAM adapter',
       configSchema,
       getAdapterClass: () => import('./CramAdapter').then(r => r.default),
     })

package/src/GuessAlignmentsTypes/index.ts

@@ -0,0 +1,79 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import { FileLocation } from '@jbrowse/core/util/types'
+import {
+  makeIndex,
+  makeIndexType,
+  getFileName,
+  AdapterGuesser,
+  TrackTypeGuesser,
+} from '@jbrowse/core/util/tracks'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addToExtensionPoint(
+    'Core-guessAdapterForLocation',
+    (adapterGuesser: AdapterGuesser) => {
+      return (
+        file: FileLocation,
+        index?: FileLocation,
+        adapterHint?: string,
+      ) => {
+        const regexGuess = /\.cram$/i
+        const adapterName = 'CramAdapter'
+        const fileName = getFileName(file)
+        const obj = {
+          type: adapterName,
+          cramLocation: file,
+          craiLocation: index || makeIndex(file, '.crai'),
+        }
+        if (regexGuess.test(fileName) && !adapterHint) {
+          return obj
+        } else if (adapterHint === adapterName) {
+          return obj
+        }
+        return adapterGuesser(file, index, adapterHint)
+      }
+    },
+  )
+
+  pluginManager.addToExtensionPoint(
+    'Core-guessAdapterForLocation',
+    (adapterGuesser: AdapterGuesser) => {
+      return (
+        file: FileLocation,
+        index?: FileLocation,
+        adapterHint?: string,
+      ) => {
+        const regexGuess = /\.bam$/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: TrackTypeGuesser) => {
+      return (adapterName: string) => {
+        if (adapterName === 'BamAdapter' || adapterName === 'CramAdapter') {
+          return 'AlignmentsTrack'
+        }
+        return trackTypeGuesser(adapterName)
+      }
+    },
+  )
+}