VALIS-26-enable-plotting-of-ENCD-bigbed-types (#15)

ENCODE-DCC · Nov 12, 2020 · fc96a23 · fc96a23
1 parent 6d247b0
commit fc96a23
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Showing 16 changed files with 752 additions and 105 deletions.
diff --git a/@types/formats/Formats.d.ts b/@types/formats/Formats.d.ts
@@ -3,11 +3,21 @@ export declare enum GenomicFileFormat {
     BigBed = 1,
     ValisGenes = 2,
     ValisDna = 3,
-    ValisVariants = 4
+    ValisVariants = 4,
+    BigBedNarrowPeak = 5,
+    BigBedBroadPeak = 6,
+    BigBedDataTssPeak = 7,
+    BigBedDataIdrPeak = 8,
+    BigBedData3Plus = 9,
+    BigBedData6Plus = 10,
+    BigBedData9Plus = 11
 }
 export declare class Formats {
     static extensionMap: {
         [key: string]: GenomicFileFormat;
     };
-    static determineFormat(path: string): GenomicFileFormat | undefined;
+    static ENCODEBigBedMap: {
+        [key: string]: GenomicFileFormat;
+    };
+    static determineFormat(path: string, fileFormatType?: string): GenomicFileFormat | undefined;
 }
diff --git a/@types/track/TrackModel.d.ts b/@types/track/TrackModel.d.ts
@@ -10,6 +10,7 @@ export declare type TrackModel = {
     heightPx?: number;
     expandedHeightPx?: number;
     highlightLocation?: string;
+    fileFormatType?: string;
     expandable?: boolean;
     color?: Array<number>;
     styleSelector?: string;

diff --git a/@types/track/annotation/AnnotationTileLoader.d.ts b/@types/track/annotation/AnnotationTileLoader.d.ts
@@ -1,11 +1,11 @@
 import IDataSource from "../../data-source/IDataSource";
 import { Tile, TileLoader } from "../TileLoader";
-import { GeneInfo, TranscriptComponentInfo, TranscriptInfo } from "./AnnotationTypes";
+import { GeneInfo, TranscriptComponentInfo, TranscriptInfo, BigBedBroadPeakColumns, BigBedNarrowPeakColumns, BigBedTssPeakColumns, BigBedIdrPeakColumns, BigBedData3Plus, BigBedData6Plus, BigBedData9Plus } from "./AnnotationTypes";
 import { BigLoader } from "../../formats";
 import { Contig, AnnotationTrackModel } from "../..";
 export declare type Gene = GeneInfo & {
     transcripts: Array<Transcript>;
-};
+} & BigBedBroadPeakColumns & BigBedNarrowPeakColumns & BigBedTssPeakColumns & BigBedIdrPeakColumns;
 export declare type Transcript = TranscriptInfo & {
     exon: Array<TranscriptComponentInfo>;
     cds: Array<TranscriptComponentInfo>;
@@ -15,7 +15,14 @@ export declare type Transcript = TranscriptInfo & {
 declare type TilePayload = Array<Gene>;
 declare enum AnnotationFormat {
     ValisGenes = 0,
-    BigBed = 1
+    BigBed = 1,
+    BigBedDataBroadPeak = 2,
+    BigBedDataNarrowPeak = 3,
+    BigBedDataTssPeak = 4,
+    BigBedDataIdrPeak = 5,
+    BigBedData3Plus = 6,
+    BigBedData6Plus = 7,
+    BigBedData9Plus = 8
 }
 export declare class AnnotationTileLoader extends TileLoader<TilePayload, void> {
     protected readonly dataSource: IDataSource;
@@ -36,4 +43,7 @@ export declare class AnnotationTileLoader extends TileLoader<TilePayload, void>
     protected getTilePayload(tile: Tile<TilePayload>): Promise<TilePayload> | TilePayload;
     static loadValisGenesAnnotations(path: string, contig: string, startBaseIndex: number, span: number, macro: boolean): Promise<TilePayload>;
 }
+export declare const parseBigBed3Plus: (chrom: string, startBase: number, endBase: number, rest: string) => BigBedData3Plus;
+export declare const parseBigBed6Plus: (chrom: string, startBase: number, endBase: number, rest: string) => BigBedData6Plus;
+export declare const parseBigBed9Plus: (chrom: string, startBase: number, endBase: number, rest: string) => BigBedData9Plus;
 export default AnnotationTileLoader;
diff --git a/@types/track/annotation/AnnotationTypes.d.ts b/@types/track/annotation/AnnotationTypes.d.ts
@@ -30,6 +30,58 @@ export interface GeneInfo extends GenomeFeature {
     score?: number;
     color?: string;
 }
+export interface BigBedBroadPeakColumns {
+    signalValue?: number;
+    pValue?: number;
+    qValue?: number;
+}
+export interface BigBedNarrowPeakColumns {
+    signalValue?: number;
+    pValue?: number;
+    qValue?: number;
+    peak?: number;
+}
+export interface BigBedTssPeakColumns {
+    count?: number;
+    gene_id?: string;
+    gene_name?: string;
+    tss_id?: string;
+    peak_cov?: string;
+}
+export interface BigBedIdrPeakColumns {
+    localIDR?: number;
+    globalIDR?: number;
+    rep1_chromStart?: number;
+    rep1_chromEnd?: number;
+    rep1_count?: number;
+    rep2_chromStart?: number;
+    rep2_chromEnd?: number;
+    rep2_count?: number;
+}
+export interface BigBedData3Plus {
+    chr: string;
+    start: number;
+    end: number;
+}
+export interface BigBedData6Plus {
+    chr: string;
+    start: number;
+    end: number;
+    name?: string;
+    score?: number;
+    strand?: string;
+}
+export interface BigBedData9Plus {
+    chr: string;
+    start: number;
+    end: number;
+    name?: string;
+    score?: number;
+    strand?: string;
+    cdStart?: number;
+    cdEnd?: number;
+    color?: string;
+}
 export declare enum TranscriptClass {
     Unspecified = 0,
     ProteinCoding = 1,

diff --git a/dist/valis-hpgv.js b/dist/valis-hpgv.js
diff --git a/dist/valis-hpgv.js.map b/dist/valis-hpgv.js.map
diff --git a/dist/valis-hpgv.react-peer.js b/dist/valis-hpgv.react-peer.js
diff --git a/dist/valis-hpgv.react-peer.js.map b/dist/valis-hpgv.react-peer.js.map