@jbrowse/plugin-variants 3.2.0 → 3.3.0

package/esm/VariantFeatureWidget/VariantSampleGrid/VariantGenotypeFrequencyTable.js

@@ -0,0 +1,74 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
+import DataGridFlexContainer from '@jbrowse/core/ui/DataGridFlexContainer';
+import { measureGridWidth } from '@jbrowse/core/util';
+import { Checkbox, FormControlLabel, Typography } from '@mui/material';
+import { DataGrid } from '@mui/x-data-grid';
+function toP(n) {
+    return n.toPrecision(3);
+}
+export default function VariantGenotypeFrequencyTable({ rows, }) {
+    const [useCounts, setUseCounts] = useState(false);
+    const summary = {};
+    if (!useCounts) {
+        for (const row of rows) {
+            const gt = row.GT;
+            if (!summary[gt]) {
+                summary[gt] = {
+                    count: 0,
+                    GT: row.GT,
+                    genotype: row.genotype,
+                };
+            }
+            summary[gt].count++;
+        }
+    }
+    else {
+        for (const row of rows) {
+            const alleleCounts = {};
+            const alleles = row.GT.split(/[/|]/);
+            for (const allele of alleles) {
+                alleleCounts[allele] = (alleleCounts[allele] || 0) + 1;
+            }
+            const key = Object.entries(alleleCounts)
+                .map(([key, val]) => `${key}:${val}`)
+                .join(';');
+            if (!summary[key]) {
+                summary[key] = {
+                    count: 0,
+                    GT: key,
+                    genotype: row.genotype,
+                };
+            }
+            summary[key].count++;
+        }
+    }
+    const gridRows = Object.entries(summary).map(([key, val]) => ({
+        id: key,
+        ...val,
+        count: `${val.count} / ${rows.length}`,
+        frequency: `${toP((val.count / rows.length) * 100)}%`,
+    }));
+    const keys = gridRows[0] ? Object.keys(gridRows[0]) : [];
+    const widths = keys.map(e => measureGridWidth(gridRows.map(r => `${r[e]}`)));
+    return (_jsxs("div", { children: [_jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: useCounts }), label: _jsx(Typography, { variant: "body2", children: "Use allele counts instead of exact GT" }), onChange: (_, checked) => {
+                    setUseCounts(checked);
+                } }), _jsx(DataGridFlexContainer, { children: _jsx(DataGrid, { rows: gridRows, hideFooter: true, rowHeight: 25, columnHeaderHeight: 35, columns: [
+                        {
+                            field: 'GT',
+                            width: widths[0],
+                        },
+                        {
+                            field: 'count',
+                            width: widths[1],
+                        },
+                        {
+                            field: 'frequency',
+                            width: widths[2],
+                        },
+                        {
+                            field: 'genotype',
+                            width: widths[3],
+                        },
+                    ] }) })] }));
+}

package/esm/VariantFeatureWidget/VariantSampleGrid/VariantSampleGrid.d.ts

@@ -1,12 +1,6 @@
+import type { VariantFieldDescriptions } from './types';
 import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
-interface FormatRecord {
-    Description?: string;
-}
-interface Descriptions {
-    FORMAT?: Record<string, FormatRecord>;
-}
-export default function VariantSamples(props: {
+export default function VariantSampleGrid(props: {
     feature: SimpleFeatureSerialized;
-    descriptions?: Descriptions | null;
+    descriptions?: VariantFieldDescriptions | null;
 }): import("react/jsx-runtime").JSX.Element | null;
-export {};

package/esm/VariantFeatureWidget/VariantSampleGrid/VariantSampleGrid.js

@@ -1,26 +1,50 @@
-import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
 import { useState } from 'react';
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
+import { ErrorMessage } from '@jbrowse/core/ui';
+import DataGridFlexContainer from '@jbrowse/core/ui/DataGridFlexContainer';
+import { ErrorBoundary } from '@jbrowse/core/ui/ErrorBoundary';
 import { measureGridWidth } from '@jbrowse/core/util';
-import { Checkbox, FormControlLabel, Typography } from '@mui/material';
-import { DataGrid, GridToolbar } from '@mui/x-data-grid';
+import { Typography } from '@mui/material';
+import { DataGrid } from '@mui/x-data-grid';
+import Checkbox2 from '../Checkbox2';
+import VariantGenotypeFrequencyTable from './VariantGenotypeFrequencyTable';
 import SampleFilters from './VariantSampleFilters';
-export default function VariantSamples(props) {
+import { areSetsEqual } from './util';
+import { makeSimpleAltString } from '../../VcfFeature/util';
+export default function VariantSampleGrid(props) {
     var _a;
     const { feature, descriptions = {} } = props;
     const [filter, setFilter] = useState({});
+    const [showOnlyGenotypeColumns, setShowOnlyGenotypeColumns] = useState(true);
+    const [showFilters, setShowFilters] = useState(false);
     const samples = (feature.samples || {});
-    const preFilteredRows = Object.entries(samples);
+    const ALT = feature.ALT;
+    const REF = feature.REF;
+    const preFilteredRows = Object.entries(samples).map(([key, val]) => {
+        var _a, _b;
+        return [
+            key,
+            {
+                ...val,
+                GT: `${(_a = val.GT) === null || _a === void 0 ? void 0 : _a[0]}`,
+                genotype: makeSimpleAltString(`${(_b = val.GT) === null || _b === void 0 ? void 0 : _b[0]}`, REF, ALT),
+            },
+        ];
+    });
     let error;
     let rows = [];
     const filters = Object.keys(filter);
     try {
         rows = preFilteredRows
-            .map(row => {
+            .map(([key, val]) => {
             return {
-                ...Object.fromEntries(Object.entries(row[1]).map(e => [e[0], `${e[1]}`])),
-                sample: row[0],
-                id: row[0],
+                ...Object.fromEntries(Object.entries(val).map(([formatField, formatValue]) => [
+                    formatField,
+                    formatValue,
+                ])),
+                sample: key,
+                id: key,
             };
         })
             .filter(row => filters.length
@@ -33,9 +57,9 @@ export default function VariantSamples(props) {
             : true);
     }
     catch (e) {
+        console.error(e);
         error = e;
     }
-    const [checked, setChecked] = useState(false);
     const keys = ['sample', ...Object.keys(((_a = preFilteredRows[0]) === null || _a === void 0 ? void 0 : _a[1]) || {})];
     const widths = keys.map(e => measureGridWidth(rows.map(r => r[e])));
     const columns = keys.map((field, index) => {
@@ -46,16 +70,13 @@ export default function VariantSamples(props) {
             width: widths[index],
         });
     });
-    return !preFilteredRows.length ? null : (_jsxs(BaseCard, { ...props, title: "Samples", children: [error ? _jsx(Typography, { color: "error", children: `${error}` }) : null, _jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: checked, onChange: event => {
-                        setChecked(event.target.checked);
-                    } }), label: _jsx(Typography, { variant: "body2", children: "Show options" }) }), checked ? (_jsx(SampleFilters, { setFilter: setFilter, columns: columns, filter: filter })) : null, _jsx("div", { style: {
-                    display: 'flex',
-                    flexDirection: 'column',
-                }, children: _jsx(DataGrid, { rows: rows, hideFooter: rows.length < 100, columns: columns, disableRowSelectionOnClick: true, rowHeight: 25, columnHeaderHeight: 35, disableColumnMenu: true, slots: { toolbar: checked ? GridToolbar : null }, slotProps: {
-                        toolbar: {
-                            printOptions: {
-                                disableToolbarButton: true,
-                            },
-                        },
-                    } }) })] }));
+    const s1 = new Set(['sample', 'GT', 'genotype']);
+    const s2 = new Set(keys);
+    return !preFilteredRows.length ? null : (_jsxs(_Fragment, { children: [_jsx(BaseCard, { ...props, title: "Genotype frequencies", children: _jsx(ErrorBoundary, { FallbackComponent: ErrorMessage, children: _jsx(VariantGenotypeFrequencyTable, { rows: rows }) }) }), _jsxs(BaseCard, { ...props, title: "Samples", children: [error ? _jsx(Typography, { color: "error", children: `${error}` }) : null, _jsx(Checkbox2, { label: "Show filters", checked: showFilters, onChange: event => {
+                            setShowFilters(event.target.checked);
+                        } }), areSetsEqual(s1, s2) ? null : (_jsx(Checkbox2, { label: "Show only genotype columns", checked: showOnlyGenotypeColumns, onChange: event => {
+                            setShowOnlyGenotypeColumns(event.target.checked);
+                        } })), showFilters ? (_jsx(SampleFilters, { setFilter: setFilter, columns: columns, filter: filter })) : null, _jsx(DataGridFlexContainer, { children: _jsx(DataGrid, { rows: rows, hideFooter: rows.length < 100, columns: showOnlyGenotypeColumns
+                                ? columns.filter(f => s1.has(f.field))
+                                : columns, rowHeight: 25, columnHeaderHeight: 35, showToolbar: true }) })] })] }));
 }

package/esm/VariantFeatureWidget/VariantSampleGrid/types.d.ts

@@ -0,0 +1,21 @@
+export interface FrequencyTableEntry {
+    count: number;
+    GT: string;
+    genotype: string | undefined;
+}
+export type FrequencyTable = Record<string, FrequencyTableEntry>;
+export interface VariantSampleGridRow {
+    sample: string;
+    id: string;
+    GT: string;
+    [key: string]: string;
+}
+export type InfoFields = Record<string, unknown[]>;
+export type Filters = Record<string, string>;
+interface FormatRecord {
+    Description?: string;
+}
+export interface VariantFieldDescriptions {
+    FORMAT?: Record<string, FormatRecord>;
+}
+export {};

package/esm/VariantFeatureWidget/VariantSampleGrid/util.d.ts

@@ -0,0 +1 @@
+export declare function areSetsEqual<T>(set1: Set<T>, set2: Set<T>): boolean;

package/esm/VariantFeatureWidget/VariantSampleGrid/util.js

@@ -0,0 +1,11 @@
+export function areSetsEqual(set1, set2) {
+    if (set1.size !== set2.size) {
+        return false;
+    }
+    for (const item of set1) {
+        if (!set2.has(item)) {
+            return false;
+        }
+    }
+    return true;
+}

package/esm/VariantRPC/MultiVariantClusterGenotypeMatrix.d.ts

@@ -1,21 +1,8 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import type { Source } from '../shared/types';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Region } from '@jbrowse/core/util';
-interface Args {
-    adapterConfig: AnyConfigurationModel;
-    stopToken?: string;
-    statusCallback: (arg: string) => void;
-    sessionId: string;
-    headers?: Record<string, string>;
-    regions: Region[];
-    bpPerPx: number;
-    sources: Source[];
-    minorAlleleFrequencyFilter: number;
-}
+import type { ClusterGenotypeMatrixArgs } from './types';
 export declare class MultiVariantClusterGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
     name: string;
-    execute(args: Args, rpcDriverClassName: string): Promise<{
+    execute(args: ClusterGenotypeMatrixArgs, rpcDriverClassName: string): Promise<{
         clusters: {
             height: number;
             indexes: number[];
@@ -25,4 +12,3 @@ export declare class MultiVariantClusterGenotypeMatrix extends RpcMethodTypeWith
         clustersGivenK: number[][][];
     }>;
 }
-export {};

package/esm/VariantRPC/MultiVariantClusterGenotypeMatrix.js

@@ -1,5 +1,5 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import { clusterData } from './cluster';
+import { clusterData } from '@jbrowse/core/util/cluster';
 import { getGenotypeMatrix } from './getGenotypeMatrix';
 export class MultiVariantClusterGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
     constructor() {
@@ -14,13 +14,10 @@ export class MultiVariantClusterGenotypeMatrix extends RpcMethodTypeWithFiltersA
         });
         return clusterData({
             data: Object.values(matrix),
-            onProgress: a => {
-                deserializedArgs.statusCallback(`${toP(a * 100)}%`);
-            },
             stopToken: deserializedArgs.stopToken,
+            onProgress: progress => {
+                deserializedArgs.statusCallback(progress);
+            },
         });
     }
 }
-function toP(n) {
-    return Number.parseFloat(n.toPrecision(3));
-}

package/esm/VariantRPC/MultiVariantGetGenotypeMatrix.d.ts

@@ -1,19 +1,6 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import type { Source } from '../shared/types';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Region } from '@jbrowse/core/util';
-interface Args {
-    adapterConfig: AnyConfigurationModel;
-    stopToken?: string;
-    sessionId: string;
-    headers?: Record<string, string>;
-    regions: Region[];
-    bpPerPx: number;
-    sources: Source[];
-    minorAlleleFrequencyFilter: number;
-}
+import type { GetGenotypeMatrixArgs } from './types';
 export declare class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
     name: string;
-    execute(args: Args, rpcDriverClassName: string): Promise<Record<string, number[]>>;
+    execute(args: GetGenotypeMatrixArgs, rpcDriverClassName: string): Promise<Record<string, number[]>>;
 }
-export {};

package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.d.ts

@@ -1,19 +1,9 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import type { GetSimplifiedFeaturesArgs } from './types';
 import type { SampleInfo } from '../shared/types';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Region } from '@jbrowse/core/util';
-interface Args {
-    adapterConfig: AnyConfigurationModel;
-    stopToken?: string;
-    sessionId: string;
-    headers?: Record<string, string>;
-    regions: Region[];
-    bpPerPx: number;
-    minorAlleleFrequencyFilter: number;
-}
 export declare class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions {
     name: string;
-    execute(args: Args, rpcDriverClassName: string): Promise<{
+    execute(args: GetSimplifiedFeaturesArgs, rpcDriverClassName: string): Promise<{
         hasPhased: boolean;
         sampleInfo: Record<string, SampleInfo>;
         features: {
@@ -22,8 +12,8 @@ export declare class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWith
                 start: number;
                 end: number;
                 refName: string;
+                name: any;
             };
         }[];
     }>;
 }
-export {};

package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.js

@@ -1,5 +1,6 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import { forEachWithStopTokenCheck } from '@jbrowse/core/util';
 import { firstValueFrom, toArray } from 'rxjs';
 import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../shared/minorAlleleFrequencyUtils';
 export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions {
@@ -8,17 +9,21 @@ export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersA
         this.name = 'MultiVariantGetSimplifiedFeatures';
     }
     async execute(args, rpcDriverClassName) {
-        var _a, _b;
         const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const { minorAlleleFrequencyFilter, regions, adapterConfig, sessionId } = deserializedArgs;
+        const { lengthCutoffFilter, minorAlleleFrequencyFilter, regions, adapterConfig, stopToken, sessionId, } = deserializedArgs;
         const { dataAdapter } = await getAdapter(this.pluginManager, sessionId, adapterConfig);
-        const feats = await firstValueFrom(dataAdapter
-            .getFeaturesInMultipleRegions(regions, deserializedArgs)
-            .pipe(toArray()));
-        const features = getFeaturesThatPassMinorAlleleFrequencyFilter(feats, minorAlleleFrequencyFilter);
+        const features = getFeaturesThatPassMinorAlleleFrequencyFilter({
+            minorAlleleFrequencyFilter,
+            lengthCutoffFilter,
+            stopToken,
+            features: await firstValueFrom(dataAdapter
+                .getFeaturesInMultipleRegions(regions, deserializedArgs)
+                .pipe(toArray())),
+        });
         const sampleInfo = {};
         let hasPhased = false;
-        for (const { feature } of features) {
+        forEachWithStopTokenCheck(features, stopToken, ({ feature }) => {
+            var _a, _b;
             const samp = feature.get('genotypes');
             for (const [key, val] of Object.entries(samp)) {
                 const isPhased = val.includes('|');
@@ -28,7 +33,7 @@ export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersA
                     isPhased: ((_b = sampleInfo[key]) === null || _b === void 0 ? void 0 : _b.isPhased) || isPhased,
                 };
             }
-        }
+        });
         return {
             hasPhased,
             sampleInfo,
@@ -38,6 +43,7 @@ export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersA
                     start: feature.get('start'),
                     end: feature.get('end'),
                     refName: feature.get('refName'),
+                    name: feature.get('name'),
                 },
             })),
         };

package/esm/VariantRPC/getGenotypeMatrix.js

@@ -1,20 +1,25 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import { forEachWithStopTokenCheck } from '@jbrowse/core/util';
 import { firstValueFrom, toArray } from 'rxjs';
 import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../shared/minorAlleleFrequencyUtils';
 export async function getGenotypeMatrix({ pluginManager, args, }) {
-    const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, } = args;
+    const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, lengthCutoffFilter, stopToken, } = args;
     const adapter = await getAdapter(pluginManager, sessionId, adapterConfig);
     const dataAdapter = adapter.dataAdapter;
-    const feats = await firstValueFrom(dataAdapter.getFeaturesInMultipleRegions(regions, args).pipe(toArray()));
     const genotypeFactor = new Set();
-    const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter(feats, minorAlleleFrequencyFilter);
+    const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter({
+        minorAlleleFrequencyFilter,
+        lengthCutoffFilter,
+        stopToken,
+        features: await firstValueFrom(dataAdapter.getFeaturesInMultipleRegions(regions, args).pipe(toArray())),
+    });
     for (const { alleleCounts } of mafs) {
         for (const alt of alleleCounts.keys()) {
             genotypeFactor.add(alt);
         }
     }
     const rows = {};
-    for (const { feature } of mafs) {
+    forEachWithStopTokenCheck(mafs, stopToken, ({ feature }) => {
         const genotypes = feature.get('genotypes');
         for (const { name } of sources) {
             if (!rows[name]) {
@@ -47,6 +52,6 @@ export async function getGenotypeMatrix({ pluginManager, args, }) {
             }
             rows[name].push(genotypeStatus);
         }
-    }
+    });
     return rows;
 }

package/esm/VariantRPC/types.d.ts

@@ -10,4 +10,27 @@ export interface GetGenotypeMatrixArgs {
     headers?: Record<string, string>;
     regions: Region[];
     bpPerPx: number;
+    lengthCutoffFilter: number;
+}
+export interface GetSimplifiedFeaturesArgs {
+    adapterConfig: AnyConfigurationModel;
+    stopToken?: string;
+    sessionId: string;
+    headers?: Record<string, string>;
+    regions: Region[];
+    bpPerPx: number;
+    minorAlleleFrequencyFilter: number;
+    lengthCutoffFilter: number;
+}
+export interface ClusterGenotypeMatrixArgs {
+    adapterConfig: AnyConfigurationModel;
+    stopToken?: string;
+    statusCallback: (arg: string) => void;
+    sessionId: string;
+    headers?: Record<string, string>;
+    regions: Region[];
+    bpPerPx: number;
+    sources: Source[];
+    minorAlleleFrequencyFilter: number;
+    lengthCutoffFilter: number;
 }

package/esm/VcfFeature/index.js

@@ -10,7 +10,6 @@ function dataFromVariant(variant, parser) {
         description,
         type,
         name: ID === null || ID === void 0 ? void 0 : ID.join(','),
-        aliases: ID && ID.length > 1 ? ID.slice(1) : undefined,
     };
 }
 function getEnd(variant) {

package/esm/VcfFeature/util.d.ts

@@ -2,3 +2,5 @@ import type VCF from '@gmod/vcf';
 export declare function getSOTermAndDescription(ref: string, alt: string[] | undefined, parser: VCF): string[];
 export declare function getSOAndDescFromAltDefs(alt: string, parser: VCF): string[];
 export declare function getSOAndDescByExamination(ref: string, alt: string): string[];
+export declare function getMinimalDesc(ref: string, alt: string): string;
+export declare function makeSimpleAltString(genotype: string, ref: string, alt: string[]): string;

package/esm/VcfFeature/util.js

@@ -1,4 +1,5 @@
 import { parseBreakend } from '@gmod/vcf';
+import { getBpDisplayStr } from '@jbrowse/core/util';
 const altTypeToSO = {
     DEL: 'deletion',
     INS: 'insertion',
@@ -62,63 +63,158 @@ export function getSOAndDescFromAltDefs(alt, parser) {
         return [soTerm, alt];
     }
     const modAlt = alt.split(':');
-    if (modAlt.length > 1) {
-        return getSOAndDescFromAltDefs(`<${modAlt.slice(0, -1).join(':')}>`, parser);
-    }
-    return [];
+    return modAlt.length > 1
+        ? getSOAndDescFromAltDefs(`<${modAlt.slice(0, -1).join(':')}>`, parser)
+        : [];
 }
 export function getSOAndDescByExamination(ref, alt) {
     const bnd = parseBreakend(alt);
     if (bnd) {
         return ['breakend', alt];
     }
-    if (ref.length === 1 && alt.length === 1) {
+    else if (ref.length === 1 && alt.length === 1) {
         return ['SNV', makeDescriptionString('SNV', ref, alt)];
     }
-    if (alt === '<INS>') {
+    else if (alt === '<INS>') {
         return ['insertion', alt];
     }
-    if (alt === '<DEL>') {
+    else if (alt === '<DEL>') {
         return ['deletion', alt];
     }
-    if (alt === '<DUP>') {
+    else if (alt === '<DUP>') {
         return ['duplication', alt];
     }
-    if (alt === '<CNV>') {
+    else if (alt === '<CNV>') {
         return ['cnv', alt];
     }
-    if (alt === '<INV>') {
+    else if (alt === '<INV>') {
         return ['inversion', alt];
     }
-    if (alt === '<TRA>') {
+    else if (alt === '<TRA>') {
         return ['translocation', alt];
     }
-    if (alt.includes('<')) {
+    else if (alt.includes('<')) {
         return ['sv', alt];
     }
-    if (ref.length === alt.length) {
-        return ref.split('').reverse().join('') === alt
-            ? ['inversion', makeDescriptionString('inversion', ref, alt)]
-            : ['substitution', makeDescriptionString('substitution', ref, alt)];
+    else if (ref.length === alt.length) {
+        const lenRef = ref.length;
+        const lenAlt = alt.length;
+        if (lenRef > 5 || lenAlt > 5) {
+            const lena = getBpDisplayStr(lenRef);
+            const lenb = getBpDisplayStr(lenAlt);
+            return ref.split('').reverse().join('') === alt
+                ? ['inverson', makeDescriptionString('inv', lena, lenb)]
+                : ['substitution', makeDescriptionString('substitution', lena, lenb)];
+        }
+        else {
+            return ref.split('').reverse().join('') === alt
+                ? ['inversion', makeDescriptionString('inv', ref, alt)]
+                : ['substitution', makeDescriptionString('substitution', ref, alt)];
+        }
     }
-    if (ref.length <= alt.length) {
+    else if (ref.length <= alt.length) {
         const len = alt.length - ref.length;
-        const lena = len.toLocaleString('en-US');
+        const lenAlt = alt.length;
+        const lenRef = ref.length;
+        const lena = getBpDisplayStr(len);
         return [
             'insertion',
-            len > 5 ? `${lena}bp INS` : makeDescriptionString('insertion', ref, alt),
+            lenRef > 5 || lenAlt > 5
+                ? `${lena} INS`
+                : makeDescriptionString('insertion', len > 5 ? lena : ref, alt),
         ];
     }
-    if (ref.length > alt.length) {
-        const len = ref.length - alt.length;
-        const lena = len.toLocaleString('en-US');
+    else if (ref.length > alt.length) {
+        const lenRef = ref.length;
+        const lenAlt = alt.length;
+        const lena = getBpDisplayStr(lenRef - lenAlt);
         return [
             'deletion',
-            len > 5 ? `${lena}bp DEL` : makeDescriptionString('deletion', ref, alt),
+            lenRef > 5 || lenAlt > 5
+                ? `${lena} DEL`
+                : makeDescriptionString('deletion', ref, alt),
         ];
     }
-    return ['indel', makeDescriptionString('indel', ref, alt)];
+    else {
+        return ['indel', makeDescriptionString('indel', ref, alt)];
+    }
+}
+export function getMinimalDesc(ref, alt) {
+    const bnd = parseBreakend(alt);
+    if (bnd) {
+        return alt;
+    }
+    else if (ref.length === 1 && alt.length === 1) {
+        return alt;
+    }
+    else if (alt === '<INS>') {
+        return alt;
+    }
+    else if (alt === '<DEL>') {
+        return alt;
+    }
+    else if (alt === '<DUP>') {
+        return alt;
+    }
+    else if (alt === '<CNV>') {
+        return alt;
+    }
+    else if (alt === '<INV>') {
+        return alt;
+    }
+    else if (alt === '<TRA>') {
+        return alt;
+    }
+    else if (alt.includes('<')) {
+        return alt;
+    }
+    else if (ref.length === alt.length) {
+        const lenRef = ref.length;
+        const lenAlt = alt.length;
+        if (lenRef > 5 || lenAlt > 5) {
+            const lena = getBpDisplayStr(lenRef);
+            const lenb = getBpDisplayStr(lenAlt);
+            return ref.split('').reverse().join('') === alt
+                ? makeDescriptionString('inv', lena, lenb)
+                : makeDescriptionString('substitution', lena, lenb);
+        }
+        else {
+            return ref.split('').reverse().join('') === alt
+                ? makeDescriptionString('inv', ref, alt)
+                : makeDescriptionString('substitution', ref, alt);
+        }
+    }
+    else if (ref.length <= alt.length) {
+        const len = alt.length - ref.length;
+        const lenAlt = alt.length;
+        const lenRef = ref.length;
+        const lena = getBpDisplayStr(len);
+        return lenRef > 5 || lenAlt > 5
+            ? `${lena} INS`
+            : makeDescriptionString('insertion', len > 5 ? lena : ref, alt);
+    }
+    else if (ref.length > alt.length) {
+        const lenRef = ref.length;
+        const lenAlt = alt.length;
+        const lena = getBpDisplayStr(lenRef - lenAlt);
+        return lenRef > 5 || lenAlt > 5
+            ? `${lena} DEL`
+            : makeDescriptionString('deletion', ref, alt);
+    }
+    else {
+        return makeDescriptionString('indel', ref, alt);
+    }
 }
 function makeDescriptionString(soTerm, ref, alt) {
-    return `${soTerm} ${ref} -> ${alt}`;
+    return `${soTerm} ${[ref, alt].join(' -> ')}`;
+}
+export function makeSimpleAltString(genotype, ref, alt) {
+    return genotype
+        .split(/[/|]/)
+        .map(r => r === '.'
+        ? '.'
+        : +r === 0
+            ? `ref(${ref.length < 10 ? ref : getBpDisplayStr(ref.length)})`
+            : getMinimalDesc(ref, alt[+r - 1] || ''))
+        .join(genotype.includes('|') ? '|' : '/');
 }