@gmod/cram 1.7.1 → 1.7.3

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Files changed (44) hide show
  1. package/CHANGELOG.md +9 -0
  2. package/README.md +19 -240
  3. package/dist/craiIndex.d.ts +2 -2
  4. package/dist/cram-bundle.js +1 -1
  5. package/dist/cramFile/codecs/_base.d.ts +3 -3
  6. package/dist/cramFile/codecs/byteArrayLength.d.ts +1 -1
  7. package/dist/cramFile/codecs/dataSeriesTypes.d.ts +3 -3
  8. package/dist/cramFile/container/compressionScheme.d.ts +2 -2
  9. package/dist/cramFile/encoding.d.ts +11 -11
  10. package/dist/cramFile/file.d.ts +4 -4
  11. package/dist/cramFile/record.d.ts +5 -5
  12. package/dist/cramFile/record.js +1 -2
  13. package/dist/cramFile/record.js.map +1 -1
  14. package/dist/cramFile/sectionParsers.d.ts +7 -7
  15. package/dist/cramFile/slice/decodeRecord.d.ts +1 -1
  16. package/dist/cramFile/slice/decodeRecord.js +5 -1
  17. package/dist/cramFile/slice/decodeRecord.js.map +1 -1
  18. package/dist/cramFile/slice/index.d.ts +1 -1
  19. package/dist/cramFile/util.d.ts +1 -1
  20. package/dist/indexedCramFile.d.ts +2 -2
  21. package/dist/sam.d.ts +1 -1
  22. package/dist/typescript.d.ts +2 -2
  23. package/esm/craiIndex.d.ts +2 -2
  24. package/esm/cramFile/codecs/_base.d.ts +3 -3
  25. package/esm/cramFile/codecs/byteArrayLength.d.ts +1 -1
  26. package/esm/cramFile/codecs/dataSeriesTypes.d.ts +3 -3
  27. package/esm/cramFile/container/compressionScheme.d.ts +2 -2
  28. package/esm/cramFile/encoding.d.ts +11 -11
  29. package/esm/cramFile/file.d.ts +4 -4
  30. package/esm/cramFile/record.d.ts +5 -5
  31. package/esm/cramFile/record.js +1 -2
  32. package/esm/cramFile/record.js.map +1 -1
  33. package/esm/cramFile/sectionParsers.d.ts +7 -7
  34. package/esm/cramFile/slice/decodeRecord.d.ts +1 -1
  35. package/esm/cramFile/slice/decodeRecord.js +5 -1
  36. package/esm/cramFile/slice/decodeRecord.js.map +1 -1
  37. package/esm/cramFile/slice/index.d.ts +1 -1
  38. package/esm/cramFile/util.d.ts +1 -1
  39. package/esm/indexedCramFile.d.ts +2 -2
  40. package/esm/sam.d.ts +1 -1
  41. package/esm/typescript.d.ts +2 -2
  42. package/package.json +14 -14
  43. package/src/cramFile/record.ts +1 -2
  44. package/src/cramFile/slice/decodeRecord.ts +5 -1
package/dist/cramFile/codecs/_base.d.ts CHANGED
@@ -1,17 +1,17 @@
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  import CramSlice from '../slice';
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  import { CramFileBlock } from '../file';
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  import { DataType } from './dataSeriesTypes';
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- export declare type DataTypeMapping = {
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+ export type DataTypeMapping = {
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  byte: number;
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  int: number;
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  long: number;
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  byteArray: Uint8Array;
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  };
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- export declare type Cursor = {
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+ export type Cursor = {
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  bitPosition: 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7;
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  bytePosition: number;
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  };
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- export declare type Cursors = {
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+ export type Cursors = {
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  lastAlignmentStart: number;
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  coreBlock: Cursor;
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  externalBlocks: {
package/dist/cramFile/codecs/byteArrayLength.d.ts CHANGED
@@ -3,7 +3,7 @@ import { ByteArrayLengthEncoding, CramEncoding } from '../encoding';
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  import CramSlice from '../slice';
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  import { CramFileBlock } from '../file';
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  import { DataType } from './dataSeriesTypes';
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- declare type CramCodecFactory = <TData extends DataType = DataType>(encodingData: CramEncoding, dataType: TData | 'ignore') => CramCodec<TData>;
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+ type CramCodecFactory = <TData extends DataType = DataType>(encodingData: CramEncoding, dataType: TData | 'ignore') => CramCodec<TData>;
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  export default class ByteArrayStopCodec extends CramCodec<'byteArray', ByteArrayLengthEncoding['parameters']> {
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  private instantiateCodec;
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  constructor(parameters: ByteArrayLengthEncoding['parameters'], dataType: 'byteArray', instantiateCodec: CramCodecFactory);
package/dist/cramFile/codecs/dataSeriesTypes.d.ts CHANGED
@@ -1,4 +1,4 @@
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  import { CramEncoding } from '../encoding';
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- export declare type DataType = 'int' | 'byte' | 'long' | 'byteArray';
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- export declare type DataSeriesEncodingKey = 'BF' | 'CF' | 'RI' | 'RL' | 'AP' | 'RG' | 'RN' | 'MF' | 'NS' | 'NP' | 'TS' | 'NF' | 'TL' | 'FN' | 'FC' | 'FP' | 'DL' | 'BB' | 'QQ' | 'BS' | 'IN' | 'RS' | 'PD' | 'HC' | 'SC' | 'MQ' | 'BA' | 'QS' | 'TC' | 'TN';
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- export declare type DataSeriesEncodingMap = Record<DataSeriesEncodingKey, CramEncoding>;
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+ export type DataType = 'int' | 'byte' | 'long' | 'byteArray';
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+ export type DataSeriesEncodingKey = 'BF' | 'CF' | 'RI' | 'RL' | 'AP' | 'RG' | 'RN' | 'MF' | 'NS' | 'NP' | 'TS' | 'NF' | 'TL' | 'FN' | 'FC' | 'FP' | 'DL' | 'BB' | 'QQ' | 'BS' | 'IN' | 'RS' | 'PD' | 'HC' | 'SC' | 'MQ' | 'BA' | 'QS' | 'TC' | 'TN';
4
+ export type DataSeriesEncodingMap = Record<DataSeriesEncodingKey, CramEncoding>;
package/dist/cramFile/container/compressionScheme.d.ts CHANGED
@@ -34,8 +34,8 @@ declare const dataSeriesTypes: {
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  readonly QQ: "byteArray";
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  readonly TL: "int";
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  };
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- export declare type DataSeriesTypes = typeof dataSeriesTypes;
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- declare type DataSeriesCache = {
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+ export type DataSeriesTypes = typeof dataSeriesTypes;
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+ type DataSeriesCache = {
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  [K in DataSeriesEncodingKey]?: CramCodec<DataSeriesTypes[K]>;
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  };
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  export default class CramContainerCompressionScheme {
package/dist/cramFile/encoding.d.ts CHANGED
@@ -1,16 +1,16 @@
1
- export declare type NullEncoding = {
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+ export type NullEncoding = {
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  codecId: 0;
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  parametersBytes: number;
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  parameters: Record<string, never>;
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  };
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- export declare type ExternalCramEncoding = {
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+ export type ExternalCramEncoding = {
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  codecId: 1;
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  parametersBytes: number;
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  parameters: {
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  blockContentId: number;
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  };
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  };
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- export declare type GolombEncoding = {
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+ export type GolombEncoding = {
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  codecId: 2;
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  parametersBytes: number;
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  parameters: {
@@ -18,7 +18,7 @@ export declare type GolombEncoding = {
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  M: number;
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  };
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  };
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- export declare type HuffmanEncoding = {
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+ export type HuffmanEncoding = {
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  codecId: 3;
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  parametersBytes: number;
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  parameters: {
@@ -28,7 +28,7 @@ export declare type HuffmanEncoding = {
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  bitLengths: number[];
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  };
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  };
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- export declare type ByteArrayLengthEncoding = {
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+ export type ByteArrayLengthEncoding = {
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  codecId: 4;
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  parametersBytes: number;
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  parameters: {
@@ -36,7 +36,7 @@ export declare type ByteArrayLengthEncoding = {
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  valuesEncoding: CramEncoding;
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  };
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  };
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- export declare type ByteArrayStopCramEncoding = {
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+ export type ByteArrayStopCramEncoding = {
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  codecId: 5;
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  parametersBytes: number;
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  parameters: {
@@ -44,7 +44,7 @@ export declare type ByteArrayStopCramEncoding = {
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  blockContentId: number;
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  };
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  };
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- export declare type BetaEncoding = {
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+ export type BetaEncoding = {
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  codecId: 6;
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  parametersBytes: number;
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  parameters: {
@@ -52,7 +52,7 @@ export declare type BetaEncoding = {
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  length: number;
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  };
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  };
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- export declare type SubexpEncoding = {
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+ export type SubexpEncoding = {
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  codecId: 7;
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  parametersBytes: number;
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  parameters: {
@@ -60,7 +60,7 @@ export declare type SubexpEncoding = {
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  K: number;
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  };
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  };
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- export declare type GolombRiceEncoding = {
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+ export type GolombRiceEncoding = {
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  codecId: 8;
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  parametersBytes: number;
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  parameters: {
@@ -68,11 +68,11 @@ export declare type GolombRiceEncoding = {
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  log2m: number;
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  };
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  };
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- export declare type GammaEncoding = {
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+ export type GammaEncoding = {
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  codecId: 9;
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  parametersBytes: number;
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  parameters: {
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  offset: number;
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  };
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  };
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- export declare type CramEncoding = NullEncoding | ExternalCramEncoding | GolombEncoding | HuffmanEncoding | ByteArrayLengthEncoding | ByteArrayStopCramEncoding | BetaEncoding | SubexpEncoding | GolombRiceEncoding | GammaEncoding;
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+ export type CramEncoding = NullEncoding | ExternalCramEncoding | GolombEncoding | HuffmanEncoding | ByteArrayLengthEncoding | ByteArrayStopCramEncoding | BetaEncoding | SubexpEncoding | GolombRiceEncoding | GammaEncoding;
package/dist/cramFile/file.d.ts CHANGED
@@ -5,18 +5,18 @@ import CramContainer from './container';
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  import { Parser } from '@gmod/binary-parser';
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  import CramRecord from './record';
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  import { Filehandle } from './filehandle';
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- export declare type CramFileSource = {
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+ export type CramFileSource = {
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  filehandle?: Filehandle;
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  url?: string;
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  path?: string;
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  };
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- export declare type SeqFetch = (seqId: number, start: number, end: number) => Promise<string>;
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- export declare type CramFileArgs = CramFileSource & {
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+ export type SeqFetch = (seqId: number, start: number, end: number) => Promise<string>;
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+ export type CramFileArgs = CramFileSource & {
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  checkSequenceMD5: boolean;
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  cacheSize?: number;
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  seqFetch: SeqFetch;
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  };
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- export declare type CramFileBlock = BlockHeader & {
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+ export type CramFileBlock = BlockHeader & {
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  _endPosition: number;
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  contentPosition: number;
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  _size: number;
package/dist/cramFile/record.d.ts CHANGED
@@ -1,11 +1,11 @@
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  import CramContainerCompressionScheme from './container/compressionScheme';
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  import decodeRecord from './slice/decodeRecord';
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- export declare type RefRegion = {
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+ export type RefRegion = {
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  start: number;
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  end: number;
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  seq: string;
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  };
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- export declare type ReadFeature = {
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+ export type ReadFeature = {
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  code: string;
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  pos: number;
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  refPos: number;
@@ -13,7 +13,7 @@ export declare type ReadFeature = {
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  ref?: string;
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  sub?: string;
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  };
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- export declare type MateRecord = {
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+ export type MateRecord = {
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  readName?: string;
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  sequenceId: number;
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  alignmentStart: number;
@@ -23,10 +23,10 @@ export declare type MateRecord = {
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  export declare const BamFlags: readonly [readonly [1, "Paired"], readonly [2, "ProperlyPaired"], readonly [4, "SegmentUnmapped"], readonly [8, "MateUnmapped"], readonly [16, "ReverseComplemented"], readonly [32, "MateReverseComplemented"], readonly [64, "Read1"], readonly [128, "Read2"], readonly [256, "Secondary"], readonly [512, "FailedQc"], readonly [1024, "Duplicate"], readonly [2048, "Supplementary"]];
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  export declare const CramFlags: readonly [readonly [1, "PreservingQualityScores"], readonly [2, "Detached"], readonly [4, "WithMateDownstream"], readonly [8, "DecodeSequenceAsStar"]];
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  export declare const MateFlags: readonly [readonly [1, "OnNegativeStrand"], readonly [2, "Unmapped"]];
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- declare type FlagsDecoder<Type> = {
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+ type FlagsDecoder<Type> = {
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  [Property in Type as `is${Capitalize<string & Property>}`]: (flags: number) => boolean;
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  };
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- declare type FlagsEncoder<Type> = {
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+ type FlagsEncoder<Type> = {
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  [Property in Type as `set${Capitalize<string & Property>}`]: (flags: number) => number;
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  };
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  export declare const BamFlagsDecoder: FlagsDecoder<"Paired" | "ProperlyPaired" | "SegmentUnmapped" | "MateUnmapped" | "ReverseComplemented" | "MateReverseComplemented" | "Read1" | "Read2" | "Secondary" | "FailedQc" | "Duplicate" | "Supplementary"> & FlagsEncoder<"Paired" | "ProperlyPaired" | "SegmentUnmapped" | "MateUnmapped" | "ReverseComplemented" | "MateReverseComplemented" | "Read1" | "Read2" | "Secondary" | "FailedQc" | "Duplicate" | "Supplementary">;
package/dist/cramFile/record.js CHANGED
@@ -34,8 +34,7 @@ function decodeReadSequence(cramRecord, refRegion) {
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  currentReadFeature += 1;
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  if (feature.code === 'b') {
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  // specify a base pair for some reason
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- const ret = feature.data.split(',');
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- const added = String.fromCharCode(...ret);
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+ const added = feature.data;
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  bases += added;
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  regionPos += added.length;
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  }
package/dist/cramFile/record.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/dist/cramFile/sectionParsers.d.ts CHANGED
@@ -7,8 +7,8 @@ declare const cramFileDefinition: {
7
7
  parser: Parser<unknown>;
8
8
  maxLength: number;
9
9
  };
10
- export declare type CramTagDictionary = string[][];
11
- export declare type CramPreservationMap = {
10
+ export type CramTagDictionary = string[][];
11
+ export type CramPreservationMap = {
12
12
  MI: boolean;
13
13
  UI: boolean;
14
14
  PI: boolean;
@@ -18,7 +18,7 @@ export declare type CramPreservationMap = {
18
18
  SM: [number, number, number, number, number];
19
19
  TD: CramTagDictionary;
20
20
  };
21
- export declare type MappedSliceHeader = {
21
+ export type MappedSliceHeader = {
22
22
  refSeqId: number;
23
23
  refSeqStart: number;
24
24
  refSeqSpan: number;
@@ -30,7 +30,7 @@ export declare type MappedSliceHeader = {
30
30
  refBaseBlockId: number;
31
31
  md5: TupleOf<number, 16>;
32
32
  };
33
- export declare type UnmappedSliceHeader = {
33
+ export type UnmappedSliceHeader = {
34
34
  numRecords: number;
35
35
  recordCounter: number;
36
36
  numBlocks: number;
@@ -39,15 +39,15 @@ export declare type UnmappedSliceHeader = {
39
39
  md5: TupleOf<number, 16>;
40
40
  };
41
41
  export declare function isMappedSliceHeader(header: MappedSliceHeader | UnmappedSliceHeader): header is MappedSliceHeader;
42
- export declare type CompressionMethod = 'raw' | 'gzip' | 'bzip2' | 'lzma' | 'rans' | 'rans4x16' | 'arith' | 'fqzcomp' | 'tok3';
43
- export declare type BlockHeader = {
42
+ export type CompressionMethod = 'raw' | 'gzip' | 'bzip2' | 'lzma' | 'rans' | 'rans4x16' | 'arith' | 'fqzcomp' | 'tok3';
43
+ export type BlockHeader = {
44
44
  compressionMethod: CompressionMethod;
45
45
  contentType: 'FILE_HEADER' | 'COMPRESSION_HEADER' | 'MAPPED_SLICE_HEADER' | 'UNMAPPED_SLICE_HEADER' | 'EXTERNAL_DATA' | 'CORE_DATA';
46
46
  contentId: number;
47
47
  compressedSize: number;
48
48
  uncompressedSize: number;
49
49
  };
50
- export declare type CramCompressionHeader = ParsedItem<{
50
+ export type CramCompressionHeader = ParsedItem<{
51
51
  preservation: CramPreservationMap;
52
52
  dataSeriesEncoding: DataSeriesEncodingMap;
53
53
  tagEncoding: Record<string, CramEncoding>;
package/dist/cramFile/slice/decodeRecord.d.ts CHANGED
@@ -4,7 +4,7 @@ import CramContainerCompressionScheme, { DataSeriesTypes } from '../container/co
4
4
  import { CramFileBlock } from '../file';
5
5
  import { Cursors, DataTypeMapping } from '../codecs/_base';
6
6
  import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes';
7
- export declare type DataSeriesDecoder = <T extends DataSeriesEncodingKey>(dataSeriesName: T) => DataTypeMapping[DataSeriesTypes[T]];
7
+ export type DataSeriesDecoder = <T extends DataSeriesEncodingKey>(dataSeriesName: T) => DataTypeMapping[DataSeriesTypes[T]];
8
8
  export default function decodeRecord(slice: CramSlice, decodeDataSeries: DataSeriesDecoder, compressionScheme: CramContainerCompressionScheme, sliceHeader: SliceHeader, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors, majorVersion: number, recordNumber: number): {
9
9
  readLength: number;
10
10
  sequenceId: number;
package/dist/cramFile/slice/decodeRecord.js CHANGED
@@ -120,7 +120,11 @@ function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries,
120
120
  return String.fromCharCode(data);
121
121
  }
122
122
  if (type === 'string') {
123
- return data.toString('utf8');
123
+ let r = '';
124
+ for (let i = 0; i < data.byteLength; i++) {
125
+ r += String.fromCharCode(data[i]);
126
+ }
127
+ return r;
124
128
  }
125
129
  if (type === 'numArray') {
126
130
  return data.toArray();
package/dist/cramFile/slice/decodeRecord.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/dist/cramFile/slice/index.d.ts CHANGED
@@ -2,7 +2,7 @@ import CramRecord from '../record';
2
2
  import CramContainer from '../container';
3
3
  import { CramFileBlock } from '../file';
4
4
  import { MappedSliceHeader, UnmappedSliceHeader } from '../sectionParsers';
5
- export declare type SliceHeader = CramFileBlock & {
5
+ export type SliceHeader = CramFileBlock & {
6
6
  parsedContent: MappedSliceHeader | UnmappedSliceHeader;
7
7
  };
8
8
  export default class CramSlice {
package/dist/cramFile/util.d.ts CHANGED
@@ -2,7 +2,7 @@
2
2
  import { Parser } from '@gmod/binary-parser';
3
3
  export declare function itf8Size(v: number): 1 | 2 | 3 | 4 | 5;
4
4
  export declare function parseItf8(buffer: Uint8Array, initialOffset: number): [number, number];
5
- export declare type ParsedItem<T> = T & {
5
+ export type ParsedItem<T> = T & {
6
6
  _endPosition: number;
7
7
  _size: number;
8
8
  };
package/dist/indexedCramFile.d.ts CHANGED
@@ -3,12 +3,12 @@ import CramRecord from './cramFile/record';
3
3
  import { SeqFetch } from './cramFile/file';
4
4
  import { Filehandle } from './cramFile/filehandle';
5
5
  import { Slice } from './craiIndex';
6
- export declare type CramFileSource = {
6
+ export type CramFileSource = {
7
7
  cramFilehandle?: Filehandle;
8
8
  cramUrl?: string;
9
9
  cramPath?: string;
10
10
  };
11
- export declare type CramIndexLike = {
11
+ export type CramIndexLike = {
12
12
  getEntriesForRange: (seqId: number, start: number, end: number) => Promise<Slice[]>;
13
13
  hasDataForReferenceSequence: (seqId: number) => Promise<boolean>;
14
14
  };
package/dist/sam.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- export declare type HeaderDataItem = {
1
+ export type HeaderDataItem = {
2
2
  tag: string;
3
3
  data: Array<{
4
4
  tag: string;
package/dist/typescript.d.ts CHANGED
@@ -1,3 +1,3 @@
1
1
  export declare function ensureNotNullish<T>(x: T | null | undefined): T;
2
- export declare type TupleOf<T, N extends number> = N extends N ? number extends N ? T[] : _TupleOf<T, N, []> : never;
3
- export declare type _TupleOf<T, N extends number, R extends unknown[]> = R['length'] extends N ? R : _TupleOf<T, N, [T, ...R]>;
2
+ export type TupleOf<T, N extends number> = N extends N ? number extends N ? T[] : _TupleOf<T, N, []> : never;
3
+ export type _TupleOf<T, N extends number, R extends unknown[]> = R['length'] extends N ? R : _TupleOf<T, N, [T, ...R]>;
package/esm/craiIndex.d.ts CHANGED
@@ -1,12 +1,12 @@
1
1
  import { CramFileSource } from './cramFile/file';
2
- export declare type Slice = {
2
+ export type Slice = {
3
3
  start: number;
4
4
  span: number;
5
5
  containerStart: number;
6
6
  sliceStart: number;
7
7
  sliceBytes: number;
8
8
  };
9
- declare type ParsedIndex = Record<string, Slice[]>;
9
+ type ParsedIndex = Record<string, Slice[]>;
10
10
  export default class CraiIndex {
11
11
  private _parseCache;
12
12
  private filehandle;
package/esm/cramFile/codecs/_base.d.ts CHANGED
@@ -1,17 +1,17 @@
1
1
  import CramSlice from '../slice';
2
2
  import { CramFileBlock } from '../file';
3
3
  import { DataType } from './dataSeriesTypes';
4
- export declare type DataTypeMapping = {
4
+ export type DataTypeMapping = {
5
5
  byte: number;
6
6
  int: number;
7
7
  long: number;
8
8
  byteArray: Uint8Array;
9
9
  };
10
- export declare type Cursor = {
10
+ export type Cursor = {
11
11
  bitPosition: 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7;
12
12
  bytePosition: number;
13
13
  };
14
- export declare type Cursors = {
14
+ export type Cursors = {
15
15
  lastAlignmentStart: number;
16
16
  coreBlock: Cursor;
17
17
  externalBlocks: {
package/esm/cramFile/codecs/byteArrayLength.d.ts CHANGED
@@ -3,7 +3,7 @@ import { ByteArrayLengthEncoding, CramEncoding } from '../encoding';
3
3
  import CramSlice from '../slice';
4
4
  import { CramFileBlock } from '../file';
5
5
  import { DataType } from './dataSeriesTypes';
6
- declare type CramCodecFactory = <TData extends DataType = DataType>(encodingData: CramEncoding, dataType: TData | 'ignore') => CramCodec<TData>;
6
+ type CramCodecFactory = <TData extends DataType = DataType>(encodingData: CramEncoding, dataType: TData | 'ignore') => CramCodec<TData>;
7
7
  export default class ByteArrayStopCodec extends CramCodec<'byteArray', ByteArrayLengthEncoding['parameters']> {
8
8
  private instantiateCodec;
9
9
  constructor(parameters: ByteArrayLengthEncoding['parameters'], dataType: 'byteArray', instantiateCodec: CramCodecFactory);
package/esm/cramFile/codecs/dataSeriesTypes.d.ts CHANGED
@@ -1,4 +1,4 @@
1
1
  import { CramEncoding } from '../encoding';
2
- export declare type DataType = 'int' | 'byte' | 'long' | 'byteArray';
3
- export declare type DataSeriesEncodingKey = 'BF' | 'CF' | 'RI' | 'RL' | 'AP' | 'RG' | 'RN' | 'MF' | 'NS' | 'NP' | 'TS' | 'NF' | 'TL' | 'FN' | 'FC' | 'FP' | 'DL' | 'BB' | 'QQ' | 'BS' | 'IN' | 'RS' | 'PD' | 'HC' | 'SC' | 'MQ' | 'BA' | 'QS' | 'TC' | 'TN';
4
- export declare type DataSeriesEncodingMap = Record<DataSeriesEncodingKey, CramEncoding>;
2
+ export type DataType = 'int' | 'byte' | 'long' | 'byteArray';
3
+ export type DataSeriesEncodingKey = 'BF' | 'CF' | 'RI' | 'RL' | 'AP' | 'RG' | 'RN' | 'MF' | 'NS' | 'NP' | 'TS' | 'NF' | 'TL' | 'FN' | 'FC' | 'FP' | 'DL' | 'BB' | 'QQ' | 'BS' | 'IN' | 'RS' | 'PD' | 'HC' | 'SC' | 'MQ' | 'BA' | 'QS' | 'TC' | 'TN';
4
+ export type DataSeriesEncodingMap = Record<DataSeriesEncodingKey, CramEncoding>;
package/esm/cramFile/container/compressionScheme.d.ts CHANGED
@@ -34,8 +34,8 @@ declare const dataSeriesTypes: {
34
34
  readonly QQ: "byteArray";
35
35
  readonly TL: "int";
36
36
  };
37
- export declare type DataSeriesTypes = typeof dataSeriesTypes;
38
- declare type DataSeriesCache = {
37
+ export type DataSeriesTypes = typeof dataSeriesTypes;
38
+ type DataSeriesCache = {
39
39
  [K in DataSeriesEncodingKey]?: CramCodec<DataSeriesTypes[K]>;
40
40
  };
41
41
  export default class CramContainerCompressionScheme {
package/esm/cramFile/encoding.d.ts CHANGED
@@ -1,16 +1,16 @@
1
- export declare type NullEncoding = {
1
+ export type NullEncoding = {
2
2
  codecId: 0;
3
3
  parametersBytes: number;
4
4
  parameters: Record<string, never>;
5
5
  };
6
- export declare type ExternalCramEncoding = {
6
+ export type ExternalCramEncoding = {
7
7
  codecId: 1;
8
8
  parametersBytes: number;
9
9
  parameters: {
10
10
  blockContentId: number;
11
11
  };
12
12
  };
13
- export declare type GolombEncoding = {
13
+ export type GolombEncoding = {
14
14
  codecId: 2;
15
15
  parametersBytes: number;
16
16
  parameters: {
@@ -18,7 +18,7 @@ export declare type GolombEncoding = {
18
18
  M: number;
19
19
  };
20
20
  };
21
- export declare type HuffmanEncoding = {
21
+ export type HuffmanEncoding = {
22
22
  codecId: 3;
23
23
  parametersBytes: number;
24
24
  parameters: {
@@ -28,7 +28,7 @@ export declare type HuffmanEncoding = {
28
28
  bitLengths: number[];
29
29
  };
30
30
  };
31
- export declare type ByteArrayLengthEncoding = {
31
+ export type ByteArrayLengthEncoding = {
32
32
  codecId: 4;
33
33
  parametersBytes: number;
34
34
  parameters: {
@@ -36,7 +36,7 @@ export declare type ByteArrayLengthEncoding = {
36
36
  valuesEncoding: CramEncoding;
37
37
  };
38
38
  };
39
- export declare type ByteArrayStopCramEncoding = {
39
+ export type ByteArrayStopCramEncoding = {
40
40
  codecId: 5;
41
41
  parametersBytes: number;
42
42
  parameters: {
@@ -44,7 +44,7 @@ export declare type ByteArrayStopCramEncoding = {
44
44
  blockContentId: number;
45
45
  };
46
46
  };
47
- export declare type BetaEncoding = {
47
+ export type BetaEncoding = {
48
48
  codecId: 6;
49
49
  parametersBytes: number;
50
50
  parameters: {
@@ -52,7 +52,7 @@ export declare type BetaEncoding = {
52
52
  length: number;
53
53
  };
54
54
  };
55
- export declare type SubexpEncoding = {
55
+ export type SubexpEncoding = {
56
56
  codecId: 7;
57
57
  parametersBytes: number;
58
58
  parameters: {
@@ -60,7 +60,7 @@ export declare type SubexpEncoding = {
60
60
  K: number;
61
61
  };
62
62
  };
63
- export declare type GolombRiceEncoding = {
63
+ export type GolombRiceEncoding = {
64
64
  codecId: 8;
65
65
  parametersBytes: number;
66
66
  parameters: {
@@ -68,11 +68,11 @@ export declare type GolombRiceEncoding = {
68
68
  log2m: number;
69
69
  };
70
70
  };
71
- export declare type GammaEncoding = {
71
+ export type GammaEncoding = {
72
72
  codecId: 9;
73
73
  parametersBytes: number;
74
74
  parameters: {
75
75
  offset: number;
76
76
  };
77
77
  };
78
- export declare type CramEncoding = NullEncoding | ExternalCramEncoding | GolombEncoding | HuffmanEncoding | ByteArrayLengthEncoding | ByteArrayStopCramEncoding | BetaEncoding | SubexpEncoding | GolombRiceEncoding | GammaEncoding;
78
+ export type CramEncoding = NullEncoding | ExternalCramEncoding | GolombEncoding | HuffmanEncoding | ByteArrayLengthEncoding | ByteArrayStopCramEncoding | BetaEncoding | SubexpEncoding | GolombRiceEncoding | GammaEncoding;
package/esm/cramFile/file.d.ts CHANGED
@@ -5,18 +5,18 @@ import CramContainer from './container';
5
5
  import { Parser } from '@gmod/binary-parser';
6
6
  import CramRecord from './record';
7
7
  import { Filehandle } from './filehandle';
8
- export declare type CramFileSource = {
8
+ export type CramFileSource = {
9
9
  filehandle?: Filehandle;
10
10
  url?: string;
11
11
  path?: string;
12
12
  };
13
- export declare type SeqFetch = (seqId: number, start: number, end: number) => Promise<string>;
14
- export declare type CramFileArgs = CramFileSource & {
13
+ export type SeqFetch = (seqId: number, start: number, end: number) => Promise<string>;
14
+ export type CramFileArgs = CramFileSource & {
15
15
  checkSequenceMD5: boolean;
16
16
  cacheSize?: number;
17
17
  seqFetch: SeqFetch;
18
18
  };
19
- export declare type CramFileBlock = BlockHeader & {
19
+ export type CramFileBlock = BlockHeader & {
20
20
  _endPosition: number;
21
21
  contentPosition: number;
22
22
  _size: number;