Alignment track and fixes on track class

Signed-off-by: eternal-flame-AD <[email protected]>

js/igv.d.ts

@@ -6,15 +6,18 @@ declare class Opaque<N extends string> {
     private readonly __opaque_brand: N;
 }
 
-export type Track = Tracks.TrackCommonOptions &
+export type TrackLoad = Tracks.TrackCommonOptions &
     ((Tracks.AnnotationTrackOptions & Tracks.TypeFormatPair<'annotation', Tracks.AnnotationFormat>) |
         (Tracks.WigTrackOptions & Tracks.TypeFormatPair<'wig', Tracks.WigFormat>) |
         (Tracks.WigMergedTrackOptions & { type: 'merged' }) |
+        (Tracks.AlignmentTrackOptions & Tracks.TypeFormatPair<'alignment', Tracks.AlignmentFormat>) |
         (Tracks.VariantTrackOptions & Tracks.TypeFormatPair<'variant', Tracks.VariantFormat>) |
         (Tracks.SegTrackOptions & Tracks.TypeFormatPair<'seg', Tracks.SegTrackFormat>) |
         (Tracks.CnvPyTorTrackOptions & Tracks.TypeFormatPair<'cnvpytor', Tracks.CnvPyTorFormat>));
 
 export namespace Tracks {
+    export declare class Track { }; \
+
     export interface TypeFormatPair<K extends string, F extends string> {
         type?: K;
         format?: F;
@@ -283,6 +286,71 @@ export namespace Tracks {
         colors?: string[];
     }
 
+    export type AlignmentFormat = "bam" | "cram";
+
+    type AlignmentBy = (string & {}) // tag:tagName and base:position
+
+    export type AlignmentSortOptions = {
+        chr: string;
+        position: number;
+        direction?: "ASC" | "DESC";
+    } & ({
+        option: "BASE" | "STRAND" | "INSERT_SIZE" | "MATR_CHR" | "MQ";
+    } | {
+        option: "TAG";
+        tag: string;
+    });
+
+    export type AlignmentTrackOptions = {
+        showCoverage?: boolean;
+        showAlignments?: boolean;
+        viewAsPairs?: boolean;
+        pairsSupported?: boolean;
+        coverageColor?: string;
+        color?: string;
+        deletionColor?: string;
+        displayMode?: "FULL" | "EXPANDED" | "SQUISHED";
+        groupBy?:
+        "strand" | "firstOfPairStrand" | "pairOrientation" | "mateChr" | "chimeric" | "supplementary" | "readOrder" | AlignmentBy;
+        samplingWindowSize?: number;
+        samplingDepth?: number;
+        alignmentRowHeight?: number;
+        readGroup?: string;
+        sort: AlignmentSortOptions;
+        filter: {
+            vendorFailed?: boolean;
+            duplicates?: boolean;
+            secondary?: boolean;
+            supplementary?: boolean;
+            mq?: number;
+            readGroups?: string[];
+        };
+        showSoftClips?: boolean;
+        showMismatches?: boolean;
+        showAllBases?: boolean;
+        showInsertionText?: boolean;
+        insertionTextColor?: string;
+        alignmentRowHeight?: number;
+        squishedRowHeight?: number;
+    } & (
+            {
+                colorBy: "strand" | "firstOfPairStrand";
+                insertionColor?: string;
+                negStrandColor?: string;
+            } |
+            {
+                colorBy: "pairOrientation" | "tlen"
+                | "unexpectedPair"
+                | "basemod" | "basemod2"
+                | AlignmentBy;
+            }
+        )
+
+
+    export declare class AlignmentTrack extends Track {
+        setHighlightedReads(readNames: string[], color: string): void;
+        sort(options: AlignmentSortOptions): void;
+    };
 }
 
 type Nucleotide = 'A' | 'C' | 'G' | 'T' | 'N';
@@ -431,7 +499,7 @@ interface CreateOptExtras {
      * Array of configuration objects defining tracks initially displayed when app launches.
      * 
      */
-    tracks: Track[];
+    tracks: TrackLoad[];
 }
 
 export type CreateOpt = GenomeOpt & CreateOptExtras;
@@ -458,11 +526,11 @@ declare class _Browser {
     loadSessionObject(session: Opaque<'igv.js session JSON'>): void;
     loadSession(session: string): void;
     // TODO: check the return type
-    loadTrack(track: Track): Promise<any>;
+    loadTrack(track: TrackLoad): Promise<any>;
     loadSampleInfo({ url: string }): void;
     findTracks(func: (track: Track) => boolean): Track[];
     findTracks(property: string, value: any): Track[];
-    removeTRack(track: Track): void;
+    removeTrack(track: Track): void;
     removeTrackByName(trackName: string): void;
     loadROI(roi: DefineROI | DefineROI[]): void;
     clearROIs(): void;