@gmod/cram 4.0.10 → 5.0.0

package/esm/cramFile/codecs/index.d.ts

@@ -1,4 +1,4 @@
-import CramCodec from './_base';
-import { DataType } from './dataSeriesTypes';
-import { CramEncoding } from '../encoding';
+import CramCodec from './_base.ts';
+import { DataType } from './dataSeriesTypes.ts';
+import { CramEncoding } from '../encoding.ts';
 export declare function instantiateCodec<TResult extends DataType = DataType>(encodingData: CramEncoding, dataType: DataType | 'ignore'): CramCodec<TResult>;

package/esm/cramFile/codecs/index.js

@@ -1,11 +1,11 @@
-import BetaCodec from './beta';
-import ByteArrayLengthCodec from './byteArrayLength';
-import ByteArrayStopCodec from './byteArrayStop';
-import ExternalCodec from './external';
-import GammaCodec from './gamma';
-import HuffmanIntCodec from './huffman';
-import SubexpCodec from './subexp';
-import { CramUnimplementedError } from '../../errors';
+import BetaCodec from "./beta.js";
+import ByteArrayLengthCodec from "./byteArrayLength.js";
+import ByteArrayStopCodec from "./byteArrayStop.js";
+import ExternalCodec from "./external.js";
+import GammaCodec from "./gamma.js";
+import HuffmanIntCodec from "./huffman.js";
+import SubexpCodec from "./subexp.js";
+import { CramUnimplementedError } from "../../errors.js";
 const codecClasses = {
     1: ExternalCodec,
     // 2: GolombCodec,

package/esm/cramFile/codecs/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/index.ts"],"names":[],"mappings":"AACA,OAAO,SAAS,MAAM,QAAQ,CAAA;AAC9B,OAAO,oBAAoB,MAAM,mBAAmB,CAAA;AACpD,OAAO,kBAAkB,MAAM,iBAAiB,CAAA;AAEhD,OAAO,aAAa,MAAM,YAAY,CAAA;AACtC,OAAO,UAAU,MAAM,SAAS,CAAA;AAChC,OAAO,eAAe,MAAM,WAAW,CAAA;AACvC,OAAO,WAAW,MAAM,UAAU,CAAA;AAClC,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AAGrD,MAAM,YAAY,GAAG;IACnB,CAAC,EAAE,aAAa;IAChB,kBAAkB;IAClB,CAAC,EAAE,eAAe;IAClB,CAAC,EAAE,oBAAoB;IACvB,CAAC,EAAE,kBAAkB;IACrB,CAAC,EAAE,SAAS;IACZ,CAAC,EAAE,WAAW;IACd,sBAAsB;IACtB,CAAC,EAAE,UAAU;CACd,CAAA;AAED,SAAS,mBAAmB,CAAC,EAAU;IACrC,OAAQ,YAAoB,CAAC,EAAE,CAAC,CAAA;AAClC,CAAC;AAED,MAAM,UAAU,gBAAgB,CAC9B,YAA0B,EAC1B,QAA6B;IAE7B,MAAM,UAAU,GAAG,mBAAmB,CACpC,QAAQ,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,YAAY,CAAC,OAAO,CACjD,CAAA;IACD,IAAI,CAAC,UAAU,EAAE,CAAC;QAChB,MAAM,IAAI,sBAAsB,CAC9B,qCAAqC,YAAY,CAAC,OAAO,EAAE,CAC5D,CAAA;IACH,CAAC;IAED,OAAO,IAAI,UAAU,CAAC,YAAY,CAAC,UAAU,EAAE,QAAQ,EAAE,gBAAgB,CAAC,CAAA;AAC5E,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/index.ts"],"names":[],"mappings":"AACA,OAAO,SAAS,MAAM,WAAW,CAAA;AACjC,OAAO,oBAAoB,MAAM,sBAAsB,CAAA;AACvD,OAAO,kBAAkB,MAAM,oBAAoB,CAAA;AAEnD,OAAO,aAAa,MAAM,eAAe,CAAA;AACzC,OAAO,UAAU,MAAM,YAAY,CAAA;AACnC,OAAO,eAAe,MAAM,cAAc,CAAA;AAC1C,OAAO,WAAW,MAAM,aAAa,CAAA;AACrC,OAAO,EAAE,sBAAsB,EAAE,MAAM,iBAAiB,CAAA;AAGxD,MAAM,YAAY,GAAG;IACnB,CAAC,EAAE,aAAa;IAChB,kBAAkB;IAClB,CAAC,EAAE,eAAe;IAClB,CAAC,EAAE,oBAAoB;IACvB,CAAC,EAAE,kBAAkB;IACrB,CAAC,EAAE,SAAS;IACZ,CAAC,EAAE,WAAW;IACd,sBAAsB;IACtB,CAAC,EAAE,UAAU;CACd,CAAA;AAED,SAAS,mBAAmB,CAAC,EAAU;IACrC,OAAQ,YAAoB,CAAC,EAAE,CAAC,CAAA;AAClC,CAAC;AAED,MAAM,UAAU,gBAAgB,CAC9B,YAA0B,EAC1B,QAA6B;IAE7B,MAAM,UAAU,GAAG,mBAAmB,CACpC,QAAQ,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,YAAY,CAAC,OAAO,CACjD,CAAA;IACD,IAAI,CAAC,UAAU,EAAE,CAAC;QAChB,MAAM,IAAI,sBAAsB,CAC9B,qCAAqC,YAAY,CAAC,OAAO,EAAE,CAC5D,CAAA;IACH,CAAC;IAED,OAAO,IAAI,UAAU,CAAC,YAAY,CAAC,UAAU,EAAE,QAAQ,EAAE,gBAAgB,CAAC,CAAA;AAC5E,CAAC"}

package/esm/cramFile/codecs/subexp.d.ts

@@ -1,8 +1,8 @@
-import CramCodec, { Cursors } from './_base';
-import { SubexpEncoding } from '../encoding';
-import { CramFileBlock } from '../file';
-import CramSlice from '../slice';
+import CramCodec, { Cursors } from './_base.ts';
+import { SubexpEncoding } from '../encoding.ts';
+import { CramFileBlock } from '../file.ts';
+import CramSlice from '../slice/index.ts';
 export default class SubexpCodec extends CramCodec<'int', SubexpEncoding['parameters']> {
     constructor(parameters: SubexpEncoding['parameters'], dataType: 'int');
-    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number;
+    decode(_slice: CramSlice, coreDataBlock: CramFileBlock, _blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number;
 }

package/esm/cramFile/codecs/subexp.js

@@ -1,6 +1,6 @@
-import CramCodec from './_base';
-import { getBits } from './getBits';
-import { CramUnimplementedError } from '../../errors';
+import CramCodec from "./_base.js";
+import { getBits } from "./getBits.js";
+import { CramUnimplementedError } from "../../errors.js";
 export default class SubexpCodec extends CramCodec {
     constructor(parameters, dataType) {
         super(parameters, dataType);
@@ -8,7 +8,7 @@ export default class SubexpCodec extends CramCodec {
             throw new CramUnimplementedError(`${this.dataType} decoding not yet implemented by SUBEXP codec`);
         }
     }
-    decode(slice, coreDataBlock, blocksByContentId, cursors) {
+    decode(_slice, coreDataBlock, _blocksByContentId, cursors) {
         let numLeadingOnes = 0;
         while (getBits(coreDataBlock.content, cursors.coreBlock, 1)) {
             numLeadingOnes = numLeadingOnes + 1;

package/esm/cramFile/codecs/subexp.js.map

@@ -1 +1 @@
-{"version":3,"file":"subexp.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/subexp.ts"],"names":[],"mappings":"AAAA,OAAO,SAAsB,MAAM,SAAS,CAAA;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AACnC,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AAKrD,MAAM,CAAC,OAAO,OAAO,WAAY,SAAQ,SAGxC;IACC,YAAY,UAAwC,EAAE,QAAe;QACnE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,sBAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,+CAA+C,CAChE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,IAAI,cAAc,GAAG,CAAC,CAAA;QACtB,OAAO,OAAO,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,EAAE,CAAC;YAC5D,cAAc,GAAG,cAAc,GAAG,CAAC,CAAA;QACrC,CAAC;QAED,IAAI,CAAS,CAAA;QACb,IAAI,CAAS,CAAA;QACb,IAAI,cAAc,KAAK,CAAC,EAAE,CAAC;YACzB,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAA;YACrB,CAAC,GAAG,OAAO,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;QAC1D,CAAC;aAAM,CAAC;YACN,CAAC,GAAG,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1C,MAAM,IAAI,GAAG,OAAO,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;YACjE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAA;QACrB,CAAC;QAED,OAAO,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACnC,CAAC;CACF"}
+{"version":3,"file":"subexp.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/subexp.ts"],"names":[],"mappings":"AAAA,OAAO,SAAsB,MAAM,YAAY,CAAA;AAC/C,OAAO,EAAE,OAAO,EAAE,MAAM,cAAc,CAAA;AACtC,OAAO,EAAE,sBAAsB,EAAE,MAAM,iBAAiB,CAAA;AAKxD,MAAM,CAAC,OAAO,OAAO,WAAY,SAAQ,SAGxC;IACC,YAAY,UAAwC,EAAE,QAAe;QACnE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,sBAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,+CAA+C,CAChE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,MAAiB,EACjB,aAA4B,EAC5B,kBAAiD,EACjD,OAAgB;QAEhB,IAAI,cAAc,GAAG,CAAC,CAAA;QACtB,OAAO,OAAO,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,EAAE,CAAC;YAC5D,cAAc,GAAG,cAAc,GAAG,CAAC,CAAA;QACrC,CAAC;QAED,IAAI,CAAS,CAAA;QACb,IAAI,CAAS,CAAA;QACb,IAAI,cAAc,KAAK,CAAC,EAAE,CAAC;YACzB,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAA;YACrB,CAAC,GAAG,OAAO,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;QAC1D,CAAC;aAAM,CAAC;YACN,CAAC,GAAG,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1C,MAAM,IAAI,GAAG,OAAO,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;YACjE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAA;QACrB,CAAC;QAED,OAAO,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACnC,CAAC;CACF"}

package/esm/cramFile/container/compressionScheme.d.ts

@@ -1,7 +1,7 @@
-import CramCodec from '../codecs/_base';
-import { DataSeriesEncodingKey, DataSeriesEncodingMap } from '../codecs/dataSeriesTypes';
-import { CramEncoding } from '../encoding';
-import { CramCompressionHeader } from '../sectionParsers';
+import CramCodec from '../codecs/_base.ts';
+import { DataSeriesEncodingKey, DataSeriesEncodingMap } from '../codecs/dataSeriesTypes.ts';
+import { CramEncoding } from '../encoding.ts';
+import { CramCompressionHeader } from '../sectionParsers.ts';
 declare const dataSeriesTypes: {
     readonly BF: "int";
     readonly CF: "int";

package/esm/cramFile/container/compressionScheme.js

@@ -1,5 +1,5 @@
-import { CramMalformedError } from '../../errors';
-import { instantiateCodec } from '../codecs';
+import { CramMalformedError } from "../../errors.js";
+import { instantiateCodec } from "../codecs/index.js";
 // the hardcoded data type to be decoded for each core
 // data field
 const dataSeriesTypes = {

package/esm/cramFile/container/compressionScheme.js.map

@@ -1 +1 @@
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+{"version":3,"file":"compressionScheme.js","sourceRoot":"","sources":["../../../src/cramFile/container/compressionScheme.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,iBAAiB,CAAA;AAMpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAA;AAIrD,sDAAsD;AACtD,aAAa;AACb,MAAM,eAAe,GAAG;IACtB,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,KAAK;IACT,gBAAgB;IAChB,gBAAgB;CACR,CAAA;AAIV,SAAS,uBAAuB,CAAC,SAAmB;IAClD,MAAM,MAAM,GAAe,IAAI,KAAK,CAAC,CAAC,CAAC,CAAA;IACvC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QAC9B,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,CAAC,CAAC,CAAA;IAC1B,CAAC;IAED,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAE1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAE1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAE1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAE1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAE1C,OAAO,MAAM,CAAA;AACf,CAAC;AAMD,MAAM,CAAC,OAAO,OAAO,8BAA8B;IAWjD,YAAY,OAA8B;QALnC,yBAAoB,GAAoB,EAAE,CAAA;QAC1C,kBAAa,GAA8B,EAAE,CAAA;QAC7C,gBAAW,GAAiC,EAAE,CAAA;QAInD,iEAAiE;QACjE,IAAI,CAAC,iBAAiB,GAAG,OAAO,CAAC,YAAY,CAAC,EAAE,CAAA;QAChD,IAAI,CAAC,OAAO,GAAG,OAAO,CAAC,YAAY,CAAC,EAAE,CAAA;QACtC,IAAI,CAAC,iBAAiB,GAAG,CAAC,CAAC,OAAO,CAAC,YAAY,CAAC,EAAE,CAAA;QAClD,IAAI,CAAC,gBAAgB,GAAG,OAAO,CAAC,YAAY,CAAC,EAAE,CAAA;QAC/C,IAAI,CAAC,kBAAkB,GAAG,uBAAuB,CAAC,OAAO,CAAC,YAAY,CAAC,EAAE,CAAC,CAAA;QAC1E,IAAI,CAAC,kBAAkB,GAAG,OAAO,CAAC,kBAAkB,CAAA;QACpD,IAAI,CAAC,WAAW,GAAG,OAAO,CAAC,WAAW,CAAA;IACxC,CAAC;IAED;;;OAGG;IACH,cAAc,CAAC,OAAe;QAC5B,MAAM,IAAI,GAAG,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;QACxC,IAAI,CAAC,IAAI,EAAE,CAAC;YACV,MAAM,YAAY,GAAG,IAAI,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YAC9C,IAAI,CAAC,YAAY,EAAE,CAAC;gBAClB,MAAM,IAAI,KAAK,CAAC,wBAAwB,CAAC,CAAA;YAC3C,CAAC;YACD,MAAM,GAAG,GAAG,gBAAgB,CAC1B,YAAY,EACZ,WAAW,CACZ,CAAA;YACD,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,GAAG,CAAA;YACjC,OAAO,GAAG,CAAA;QACZ,CAAC;aAAM,CAAC;YACN,OAAO,IAAI,CAAA;QACb,CAAC;IACH,CAAC;IAED;;;;OAIG;IACH,WAAW,CAAC,SAAiB;QAC3B,OAAO,IAAI,CAAC,gBAAgB,CAAC,SAAS,CAAC,CAAA;IACzC,CAAC;IAED,qBAAqB,CACnB,cAA2B;QAE3B,IAAI,CAAC,GACH,IAAI,CAAC,oBAAoB,CAAC,cAAc,CAAC,CAAA;QAC3C,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;YACpB,MAAM,YAAY,GAAG,IAAI,CAAC,kBAAkB,CAAC,cAAc,CAAC,CAAA;YAC5D,uEAAuE;YACvE,IAAI,YAAY,EAAE,CAAC;gBACjB,MAAM,QAAQ,GAAG,eAAe,CAAC,cAAc,CAAC,CAAA;gBAChD,uEAAuE;gBACvE,IAAI,CAAC,QAAQ,EAAE,CAAC;oBACd,MAAM,IAAI,kBAAkB,CAC1B,oBAAoB,cAAc,yCAAyC,CAC5E,CAAA;gBACH,CAAC;gBACD,CAAC,GAAG,gBAAgB,CAAC,YAAY,EAAE,QAAQ,CAAC,CAAA;gBAC5C,+CAA+C;gBAC/C,IAAI,CAAC,oBAAoB,CAAC,cAAc,CAAC,GAAG,CAAmB,CAAA;YACjE,CAAC;QACH,CAAC;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,MAAM;QACJ,MAAM,IAAI,GAAQ,EAAE,CAAA;QACpB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YAC5B,IAAI,CAAC,CAAC,QAAQ,CAAC,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package/esm/cramFile/container/index.d.ts

@@ -1,6 +1,6 @@
-import CramSlice from '../slice';
-import CramContainerCompressionScheme from './compressionScheme';
-import CramFile from '../file';
+import CramSlice from '../slice/index.ts';
+import CramContainerCompressionScheme from './compressionScheme.ts';
+import CramFile from '../file.ts';
 export default class CramContainer {
     file: CramFile;
     filePosition: number;
@@ -22,14 +22,14 @@ export default class CramContainer {
     }>;
     getCompressionHeaderBlock(): Promise<{
         parsedContent: {
-            dataSeriesEncoding: import("../codecs/dataSeriesTypes").DataSeriesEncodingMap;
-            preservation: import("../sectionParsers").CramPreservationMap;
-            tagEncoding: Record<string, import("../encoding").CramEncoding>;
+            dataSeriesEncoding: import("../codecs/dataSeriesTypes.ts").DataSeriesEncodingMap;
+            preservation: import("../sectionParsers.ts").CramPreservationMap;
+            tagEncoding: Record<string, import("../encoding.ts").CramEncoding>;
         } & {
             _endPosition: number;
             _size: number;
         };
-        compressionMethod: import("../sectionParsers").CompressionMethod;
+        compressionMethod: import("../sectionParsers.ts").CompressionMethod;
         contentType: "FILE_HEADER" | "COMPRESSION_HEADER" | "MAPPED_SLICE_HEADER" | "UNMAPPED_SLICE_HEADER" | "EXTERNAL_DATA" | "CORE_DATA";
         contentId: number;
         compressedSize: number;
@@ -40,7 +40,7 @@ export default class CramContainer {
         content: Uint8Array;
         crc32?: number;
     } | null>;
-    getFirstBlock(): Promise<import("../file").CramFileBlock>;
+    getFirstBlock(): Promise<import("../file.ts").CramFileBlock>;
     getCompressionScheme(): Promise<CramContainerCompressionScheme | undefined>;
     getSlice(slicePosition: number, sliceSize: number): CramSlice;
     _readContainerHeader(position: number): Promise<{

package/esm/cramFile/container/index.js

@@ -1,9 +1,8 @@
-import { CramMalformedError } from '../../errors';
-// locals
-import CramSlice from '../slice';
-import { itf8Size, parseItem, tinyMemoize } from '../util';
-import CramContainerCompressionScheme from './compressionScheme';
-import { getSectionParsers } from '../sectionParsers';
+import { CramMalformedError } from "../../errors.js";
+import CramSlice from "../slice/index.js";
+import { itf8Size, parseItem, tinyMemoize } from "../util.js";
+import CramContainerCompressionScheme from "./compressionScheme.js";
+import { getSectionParsers } from "../sectionParsers.js";
 export default class CramContainer {
     constructor(file, filePosition) {
         this.file = file;

package/esm/cramFile/container/index.js.map

@@ -1 +1 @@
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package/esm/cramFile/file.d.ts

@@ -1,7 +1,7 @@
 import QuickLRU from 'quick-lru';
-import CramContainer from './container';
-import CramRecord from './record';
-import { BlockHeader, CompressionMethod } from './sectionParsers';
+import CramContainer from './container/index.ts';
+import CramRecord from './record.ts';
+import { BlockHeader, CompressionMethod } from './sectionParsers.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
 export interface CramFileSource {
     filehandle?: GenericFilehandle;

package/esm/cramFile/file.js

@@ -1,16 +1,16 @@
 import crc32 from 'crc/calculators/crc32';
 import QuickLRU from 'quick-lru';
 import { XzReadableStream } from 'xz-decompress';
-import { CramMalformedError, CramUnimplementedError } from '../errors';
-import * as htscodecs from '../htscodecs';
-import { open } from '../io';
-import ransuncompress from '../rans';
-import { parseHeaderText } from '../sam';
-import { decode } from '../seek-bzip';
-import { unzip } from '../unzip';
-import CramContainer from './container';
-import { cramFileDefinition, getSectionParsers, } from './sectionParsers';
-import { parseItem, tinyMemoize } from './util';
+import { CramMalformedError, CramUnimplementedError } from "../errors.js";
+import * as htscodecs from "../htscodecs/index.js";
+import { open } from "../io.js";
+import ransuncompress from "../rans/index.js";
+import { parseHeaderText } from "../sam.js";
+import { decode } from "../seek-bzip/index.js";
+import { unzip } from "../unzip.js";
+import CramContainer from "./container/index.js";
+import { cramFileDefinition, getSectionParsers, } from "./sectionParsers.js";
+import { parseItem, tinyMemoize } from "./util.js";
 function bufferToStream(buf) {
     return new ReadableStream({
         start(controller) {
@@ -187,11 +187,7 @@ export default class CramFile {
     async _uncompressPre(compressionMethod, inputBuffer, uncompressedSize) {
         // console.log({ compressionMethod })
         if (compressionMethod === 'gzip') {
-            const ret = unzip(inputBuffer);
-            if (ret[0] === 24) {
-                // console.log(ret.slice(0, 500).join(','))
-            }
-            return ret;
+            return unzip(inputBuffer);
         }
         else if (compressionMethod === 'bzip2') {
             return decode(inputBuffer);
@@ -204,8 +200,6 @@ export default class CramFile {
             const outputBuffer = new Uint8Array(uncompressedSize);
             ransuncompress(inputBuffer, outputBuffer);
             return outputBuffer;
-            // htscodecs r4x8 is slower, but compatible.
-            // htscodecs.r4x8_uncompress(inputBuffer, outputBuffer);
         }
         else if (compressionMethod === 'rans4x16') {
             return htscodecs.r4x16_uncompress(inputBuffer);

package/esm/cramFile/file.js.map

@@ -1 +1 @@
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package/esm/cramFile/index.d.ts

@@ -1,2 +1,2 @@
-export { default as CramRecord } from './record';
-export { default } from './file';
+export { default as CramRecord } from './record.ts';
+export { default } from './file.ts';

package/esm/cramFile/index.js

@@ -1,3 +1,3 @@
-export { default as CramRecord } from './record';
-export { default } from './file';
+export { default as CramRecord } from "./record.js";
+export { default } from "./file.js";
 //# sourceMappingURL=index.js.map

package/esm/cramFile/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cramFile/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,UAAU,CAAA;AAEhD,OAAO,EAAE,OAAO,EAAE,MAAM,QAAQ,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cramFile/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,aAAa,CAAA;AAEnD,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA"}

package/esm/cramFile/record.d.ts

@@ -1,5 +1,5 @@
-import CramContainerCompressionScheme from './container/compressionScheme';
-import type decodeRecord from './slice/decodeRecord';
+import CramContainerCompressionScheme from './container/compressionScheme.ts';
+import type decodeRecord from './slice/decodeRecord.ts';
 export interface RefRegion {
     start: number;
     end: number;

package/esm/cramFile/record.js

@@ -1,4 +1,4 @@
-import Constants from './constants';
+import Constants from "./constants.js";
 function decodeReadSequence(cramRecord, refRegion) {
     // if it has no length, it has no sequence
     if (!cramRecord.lengthOnRef && !cramRecord.readLength) {

package/esm/cramFile/record.js.map

@@ -1 +1 @@
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package/esm/cramFile/sectionParsers.d.ts

@@ -1,6 +1,6 @@
-import { TupleOf } from '../typescript';
-import { DataSeriesEncodingMap } from './codecs/dataSeriesTypes';
-import { CramEncoding } from './encoding';
+import { TupleOf } from '../typescript.ts';
+import { DataSeriesEncodingMap } from './codecs/dataSeriesTypes.ts';
+import { CramEncoding } from './encoding.ts';
 export declare function cramFileDefinition(): {
     parser: (b: Uint8Array, _startOffset?: number) => {
         value: {

package/esm/cramFile/sectionParsers.js

@@ -1,4 +1,4 @@
-import { parseItf8, parseLtf8 } from './util';
+import { parseItf8, parseLtf8 } from "./util.js";
 export function cramFileDefinition() {
     return {
         parser: (b, _startOffset = 0) => {

package/esm/cramFile/sectionParsers.js.map

@@ -1 +1 @@
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package/esm/cramFile/slice/decodeRecord.d.ts

@@ -1,9 +1,9 @@
-import { Cursors, DataTypeMapping } from '../codecs/_base';
-import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes';
-import CramContainerCompressionScheme, { DataSeriesTypes } from '../container/compressionScheme';
-import { ReadFeature } from '../record';
-import CramSlice, { SliceHeader } from './index';
-import { CramFileBlock } from '../file';
+import { Cursors, DataTypeMapping } from '../codecs/_base.ts';
+import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes.ts';
+import CramContainerCompressionScheme, { DataSeriesTypes } from '../container/compressionScheme.ts';
+import { ReadFeature } from '../record.ts';
+import CramSlice, { SliceHeader } from './index.ts';
+import { CramFileBlock } from '../file.ts';
 export type DataSeriesDecoder = <T extends DataSeriesEncodingKey>(dataSeriesName: T) => DataTypeMapping[DataSeriesTypes[T]] | undefined;
 export default function decodeRecord(slice: CramSlice, decodeDataSeries: DataSeriesDecoder, compressionScheme: CramContainerCompressionScheme, sliceHeader: SliceHeader, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors, majorVersion: number, recordNumber: number): {
     readLength: number;

package/esm/cramFile/slice/decodeRecord.js

@@ -1,6 +1,6 @@
-import { CramMalformedError } from '../../errors';
-import { BamFlagsDecoder, CramFlagsDecoder, MateFlagsDecoder, } from '../record';
-import { isMappedSliceHeader } from '../sectionParsers';
+import { CramMalformedError } from "../../errors.js";
+import { BamFlagsDecoder, CramFlagsDecoder, MateFlagsDecoder, } from "../record.js";
+import { isMappedSliceHeader } from "../sectionParsers.js";
 /**
  * given a Buffer, read a string up to the first null character
  * @private