@jbrowse/plugin-alignments 1.6.6 → 1.6.9

package/dist/BamAdapter/BamSlightlyLazyFeature.d.ts

@@ -1,13 +1,11 @@
 /// <reference types="node" />
 import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
 import { BamRecord } from '@gmod/bam';
-import { Mismatch } from './MismatchParser';
 import BamAdapter from './BamAdapter';
 export default class BamSlightlyLazyFeature implements Feature {
     private record;
     private adapter;
     private ref?;
-    private cachedMD;
     constructor(record: BamRecord, adapter: BamAdapter, ref?: string | undefined);
     _get_name(): any;
     _get_type(): string;
@@ -20,7 +18,6 @@ export default class BamSlightlyLazyFeature implements Feature {
     _get_next_refName(): string | undefined;
     _get_next_segment_position(): string | undefined;
     _get_seq(): string;
-    _get_MD(): any;
     qualRaw(): Buffer | undefined;
     set(): void;
     tags(): string[];
@@ -31,12 +28,6 @@ export default class BamSlightlyLazyFeature implements Feature {
     children(): undefined;
     pairedFeature(): boolean;
     toJSON(): SimpleFeatureSerialized;
-    _get_skips_and_dels(opts?: {
-        cigarAttributeName: string;
-    }): Mismatch[];
-    _get_mismatches({ cigarAttributeName, mdAttributeName, }?: {
-        cigarAttributeName?: string;
-        mdAttributeName?: string;
-    }): Mismatch[];
+    _get_mismatches(): import("./MismatchParser").Mismatch[];
     _get_clipPos(): number;
 }

package/dist/BamAdapter/MismatchParser.d.ts

@@ -10,15 +10,13 @@ export interface Mismatch {
     cliplen?: number;
 }
 export declare function parseCigar(cigar: string): string[];
-export declare function cigarToMismatches(ops: string[], seq: string, qual?: Buffer): Mismatch[];
+export declare function cigarToMismatches(ops: string[], seq: string, ref?: string, qual?: Buffer): Mismatch[];
 /**
  * parse a SAM MD tag to find mismatching bases of the template versus the reference
  * @returns array of mismatches and their positions
  */
-export declare function mdToMismatches(mdstring: string, cigarOps: string[], cigarMismatches: Mismatch[], seq: string, qual?: Buffer): Mismatch[];
-export declare function getTemplateCoord(refCoord: number, cigarOps: string[]): number;
-export declare function getMismatches(cigarString: string, mdString: string, seq: string, qual?: Buffer): Mismatch[];
-export declare function generateMD(target: string, query: string, cigar: string): string;
+export declare function mdToMismatches(mdstring: string, ops: string[], cigarMismatches: Mismatch[], seq: string, qual?: Buffer): Mismatch[];
+export declare function getMismatches(cigar: string, md: string, seq: string, ref?: string, qual?: Buffer): Mismatch[];
 export declare function getNextRefPos(cigarOps: string[], positions: number[]): Generator<number, void, unknown>;
 export declare function getModificationPositions(mm: string, fseq: string, fstrand: number): ({
     type: string;

package/dist/CramAdapter/CramSlightlyLazyFeature.d.ts

@@ -13,7 +13,7 @@ export interface Mismatch {
 export default class CramSlightlyLazyFeature implements Feature {
     private record;
     private _store;
-    constructor(record: any, store: CramAdapter);
+    constructor(record: any, _store: CramAdapter);
     _get_name(): any;
     _get_start(): number;
     _get_end(): number;
@@ -46,5 +46,4 @@ export default class CramSlightlyLazyFeature implements Feature {
     _get_clipPos(): any;
     toJSON(): SimpleFeatureSerialized;
     _get_mismatches(): Mismatch[];
-    _get_skips_and_dels(): Mismatch[];
 }

package/dist/LinearSNPCoverageDisplay/models/model.d.ts

@@ -26,7 +26,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
         renderInProgress: AbortController | undefined;
         filled: boolean;
         reactElement: import("react").ReactElement<any, string | ((props: any) => import("react").ReactElement<any, any> | null) | (new (props: any) => import("react").Component<any, any, any>)> | undefined;
-        features: Map<string, import("@jbrowse/core/util/simpleFeature").Feature> | undefined;
+        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
         status: string;
         error: unknown;
@@ -44,7 +44,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
         setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | ((props: any) => import("react").ReactElement<any, any> | null) | (new (props: any) => import("react").Component<any, any, any>)>;
-            features: Map<string, import("@jbrowse/core/util/simpleFeature").Feature>;
+            features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
             maxHeightReached: boolean;
             renderProps: any;

package/dist/PileupRenderer/PileupRenderer.d.ts

@@ -1,10 +1,9 @@
 /// <reference types="react" />
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
 import BoxRendererType, { RenderArgs, RenderArgsSerialized, RenderArgsDeserialized as BoxRenderArgsDeserialized, RenderResults, ResultsSerialized, ResultsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
 import { Theme } from '@material-ui/core';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { Region } from '@jbrowse/core/util/types';
+import { Region, Feature } from '@jbrowse/core/util';
 import { BaseLayout } from '@jbrowse/core/util/layouts/BaseLayout';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import { PileupLayoutSession, PileupLayoutSessionProps } from './PileupLayoutSession';
 export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
     colorBy?: {
@@ -66,16 +65,30 @@ export default class PileupRenderer extends BoxRendererType {
     getOrientation(feature: Feature, config: AnyConfigurationModel): string;
     colorByInsertSize(feature: Feature, _config: AnyConfigurationModel): string;
     colorByStranded(feature: Feature, _config: AnyConfigurationModel): "color_rev_strand" | "color_fwd_strand" | "color_rev_missing_mate" | "color_fwd_missing_mate" | "color_rev_strand_not_proper" | "color_fwd_strand_not_proper" | "color_fwd_diff_chr" | "color_rev_diff_chr";
+    colorByPerBaseLettering(ctx: CanvasRenderingContext2D, feat: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: {
+        colorForBase: Record<string, string>;
+        contrastForBase: Record<string, string>;
+        charWidth: number;
+        charHeight: number;
+    }): void;
     colorByPerBaseQuality(ctx: CanvasRenderingContext2D, feat: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number): void;
     colorByModifications(ctx: CanvasRenderingContext2D, layoutFeature: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: RenderArgsDeserializedWithFeaturesAndLayout): void;
     colorByMethylation(ctx: CanvasRenderingContext2D, layoutFeature: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: RenderArgsDeserializedWithFeaturesAndLayout): void;
     drawRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserialized): void;
     drawAlignmentRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout & {
+        colorForBase: Record<string, string>;
+        contrastForBase: Record<string, string>;
+        charWidth: number;
+        charHeight: number;
         defaultColor: boolean;
     }): void;
-    drawMismatches(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout, theme: Theme, colorForBase: {
-        [key: string]: string;
-    }, opts: {
+    drawMismatches(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout, opts: {
+        colorForBase: {
+            [key: string]: string;
+        };
+        contrastForBase: {
+            [key: string]: string;
+        };
         mismatchAlpha?: boolean;
         drawSNPs?: boolean;
         drawIndels?: boolean;
@@ -87,6 +100,7 @@ export default class PileupRenderer extends BoxRendererType {
     drawSoftClipping(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout, config: AnyConfigurationModel, theme: Theme): void;
     makeImageData(ctx: CanvasRenderingContext2D, layoutRecords: (LayoutFeature | null)[], props: RenderArgsDeserializedWithFeaturesAndLayout): Promise<void>;
     layoutFeats(props: RenderArgsDeserializedWithFeaturesAndLayout): (LayoutRecord | null)[];
+    fetchSequence(renderProps: RenderArgsDeserialized): Promise<any>;
     render(renderProps: RenderArgsDeserialized): Promise<{
         features: Map<string, Feature>;
         layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts

@@ -2,7 +2,6 @@ import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters
 import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
-import { Observable } from 'rxjs';
 interface SNPCoverageOptions extends BaseOptions {
     filters?: SerializableFilterChain;
 }
@@ -11,19 +10,12 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
         subadapter: BaseFeatureDataAdapter;
         sequenceAdapter: BaseFeatureDataAdapter | undefined;
     }>;
-    getFeatures(region: Region, opts?: SNPCoverageOptions): Observable<Feature>;
+    fetchSequence(region: Region): Promise<any>;
+    getFeatures(region: Region, opts?: SNPCoverageOptions): import("rxjs").Observable<Feature>;
     estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     freeResources(): void;
-    /**
-     * Generates coverage bins from features which details
-     * the reference, mismatches, strands, and coverage info
-     * @param features - Features of region to be passed in
-     * @param region - Region
-     * @param bpPerPx - base pairs per pixel
-     * @returns Array of nested frequency tables
-     */
-    generateCoverageBins(features: Observable<Feature>, region: Region, opts: {
+    generateCoverageBins(features: Feature[], region: Region, opts: {
         bpPerPx?: number;
         colorBy?: {
             type: string;