@gmod/cram 2.0.4 → 3.0.0

package/dist/cramFile/sectionParsers.d.ts

@@ -1,13 +1,50 @@
-import { Parser } from '@gmod/binary-parser';
 import { TupleOf } from '../typescript';
-import { ParsedItem } from './util';
 import { DataSeriesEncodingMap } from './codecs/dataSeriesTypes';
 import { CramEncoding } from './encoding';
-declare const cramFileDefinition: {
-    parser: Parser<unknown>;
+export declare function cramFileDefinition(): {
+    parser: (buffer: Buffer, _startOffset?: number) => {
+        value: {
+            magic: string;
+            majorVersion: number;
+            minorVersion: number;
+            fileId: string;
+        };
+        offset: number;
+    };
+    maxLength: number;
+};
+export declare function cramBlockHeader(): {
+    parser: (buffer: Buffer, _startOffset?: number) => {
+        offset: number;
+        value: {
+            uncompressedSize: number;
+            compressedSize: number;
+            contentId: number;
+            contentType: "FILE_HEADER" | "COMPRESSION_HEADER" | "MAPPED_SLICE_HEADER" | "UNMAPPED_SLICE_HEADER" | "EXTERNAL_DATA" | "CORE_DATA";
+            compressionMethod: CompressionMethod;
+        };
+    };
+    maxLength: number;
+};
+export declare function cramBlockCrc32(): {
+    parser: (buffer: Buffer, offset: number) => {
+        offset: number;
+        value: {
+            crc32: number;
+        };
+    };
     maxLength: number;
 };
 export type CramTagDictionary = string[][];
+export declare function cramTagDictionary(): {
+    parser: (buffer: Buffer, offset: number) => {
+        value: {
+            size: number;
+            ents: string[][];
+        };
+        offset: number;
+    };
+};
 export interface CramPreservationMap {
     MI: boolean;
     UI: boolean;
@@ -18,6 +55,25 @@ export interface CramPreservationMap {
     SM: [number, number, number, number, number];
     TD: CramTagDictionary;
 }
+export declare function cramPreservationMap(): {
+    parser: (buffer: Buffer, offset: number) => {
+        value: {
+            mapSize: number;
+            mapCount: number;
+            ents: ({
+                key: string;
+                value: boolean;
+            } | {
+                key: string;
+                value: number[];
+            } | {
+                key: string;
+                value: string[][];
+            })[];
+        };
+        offset: number;
+    };
+};
 export interface MappedSliceHeader {
     refSeqId: number;
     refSeqStart: number;
@@ -28,7 +84,7 @@ export interface MappedSliceHeader {
     numContentIds: number;
     contentIds: number[];
     refBaseBlockId: number;
-    md5: TupleOf<number, 16>;
+    md5?: TupleOf<number, 16>;
 }
 export interface UnmappedSliceHeader {
     numRecords: number;
@@ -36,9 +92,14 @@ export interface UnmappedSliceHeader {
     numBlocks: number;
     numContentIds: number;
     contentIds: number[];
-    md5: TupleOf<number, 16>;
+    md5?: TupleOf<number, 16>;
+}
+export declare function isMappedSliceHeader(header: unknown): header is MappedSliceHeader;
+interface Value {
+    codecId: number;
+    parametersBytes: number;
+    parameters: Record<string, unknown>;
 }
-export declare function isMappedSliceHeader(header: MappedSliceHeader | UnmappedSliceHeader): header is MappedSliceHeader;
 export type CompressionMethod = 'raw' | 'gzip' | 'bzip2' | 'lzma' | 'rans' | 'rans4x16' | 'arith' | 'fqzcomp' | 'tok3';
 export interface BlockHeader {
     compressionMethod: CompressionMethod;
@@ -47,63 +108,149 @@ export interface BlockHeader {
     compressedSize: number;
     uncompressedSize: number;
 }
-export type CramCompressionHeader = ParsedItem<{
+export interface CramCompressionHeader {
     preservation: CramPreservationMap;
     dataSeriesEncoding: DataSeriesEncodingMap;
     tagEncoding: Record<string, CramEncoding>;
-}>;
-declare function getSectionParsers(majorVersion: number): {
+    _size: number;
+    _endPosition: number;
+}
+export declare function getSectionParsers(majorVersion: number): {
     cramFileDefinition: {
-        parser: Parser<{
-            magic: string;
-            majorVersion: number;
-            minorVersion: number;
-            fileId: string;
-        }>;
+        parser: (buffer: Buffer, _startOffset?: number) => {
+            value: {
+                magic: string;
+                majorVersion: number;
+                minorVersion: number;
+                fileId: string;
+            };
+            offset: number;
+        };
         maxLength: number;
     };
-    cramContainerHeader1: {
-        parser: Parser<{
-            length: number;
-            refSeqId: number;
-            refSeqStart: number;
-            alignmentSpan: number;
-            numRecords: number;
-            recordCounter: number;
-            numBases: number;
-            numBlocks: number;
-            numLandmarks: number;
-        }>;
-        maxLength: number;
-    };
-    cramContainerHeader2: {
-        parser: Parser<{
-            numLandmarks: number;
-            landmarks: number[];
-            crc32: number;
-        }>;
-        maxLength: (x: number) => number;
-    };
     cramBlockHeader: {
-        parser: Parser<BlockHeader>;
+        parser: (buffer: Buffer, _startOffset?: number) => {
+            offset: number;
+            value: {
+                uncompressedSize: number;
+                compressedSize: number;
+                contentId: number;
+                contentType: "FILE_HEADER" | "COMPRESSION_HEADER" | "MAPPED_SLICE_HEADER" | "UNMAPPED_SLICE_HEADER" | "EXTERNAL_DATA" | "CORE_DATA";
+                compressionMethod: CompressionMethod;
+            };
+        };
         maxLength: number;
     };
     cramBlockCrc32: {
-        parser: Parser<{
-            crc32: number;
-        }>;
+        parser: (buffer: Buffer, offset: number) => {
+            offset: number;
+            value: {
+                crc32: number;
+            };
+        };
         maxLength: number;
     };
+    cramDataSeriesEncodingMap: {
+        parser: (buffer: Buffer, offset: number) => {
+            value: {
+                mapSize: number;
+                ents: {
+                    key: string;
+                    value: Value;
+                }[];
+                mapCount: number;
+            };
+            offset: number;
+        };
+    };
+    cramTagEncodingMap: {
+        parser: (buffer: Buffer, offset: number) => {
+            value: {
+                mapSize: number;
+                ents: {
+                    key: string;
+                    value: Value;
+                }[];
+                mapCount: number;
+            };
+            offset: number;
+        };
+    };
     cramCompressionHeader: {
-        parser: Parser<CramCompressionHeader>;
+        parser: (buffer: Buffer, offset: number) => {
+            value: {
+                dataSeriesEncoding: DataSeriesEncodingMap;
+                preservation: CramPreservationMap;
+                tagEncoding: Record<string, CramEncoding>;
+            };
+            offset: number;
+        };
     };
-    cramMappedSliceHeader: {
-        parser: Parser<MappedSliceHeader>;
-        maxLength: (numContentIds: number) => number;
+    cramEncoding: {
+        parser: (buffer: Buffer, offset: number) => {
+            value: Value;
+            offset: number;
+        };
     };
     cramUnmappedSliceHeader: {
-        parser: Parser<UnmappedSliceHeader>;
+        parser: (buffer: Buffer, offset: number) => {
+            value: {
+                recordCounter: number;
+                md5: [number, number, number, number, number, number, number, number, number, number, number, number, number, number, number, number] | undefined;
+                contentIds: number[];
+                numContentIds: number;
+                numBlocks: number;
+                numRecords: number;
+            };
+            offset: number;
+        };
+        maxLength: (numContentIds: number) => number;
+    };
+    cramMappedSliceHeader: {
+        parser: (buffer: Buffer, offset: number) => {
+            value: {
+                md5: [number, number, number, number, number, number, number, number, number, number, number, number, number, number, number, number] | undefined;
+                numBlocks: number;
+                numRecords: number;
+                numContentIds: number;
+                refSeqSpan: number;
+                refSeqId: number;
+                refSeqStart: number;
+                recordCounter: number;
+                refBaseBlockId: number;
+                contentIds: number[];
+            };
+            offset: number;
+        };
         maxLength: (numContentIds: number) => number;
     };
+    cramContainerHeader1: {
+        maxLength: number;
+        parser: (buffer: Buffer, offset: number) => {
+            value: {
+                length: number;
+                refSeqId: number;
+                refSeqStart: number;
+                alignmentSpan: number;
+                numBlocks: number;
+                numLandmarks: number;
+                numBases: number | undefined;
+                recordCounter: number;
+                numRecords: number;
+            };
+            offset: number;
+        };
+    };
+    cramContainerHeader2: {
+        parser: (buffer: Buffer, offset: number) => {
+            value: {
+                numLandmarks: number;
+                landmarks: number[];
+                crc32?: number | undefined;
+            };
+            offset: number;
+        };
+        maxLength: (numLandmarks: number) => number;
+    };
 };
-export { cramFileDefinition, getSectionParsers };
+export {};