@gmod/cram 4.0.9 → 5.0.0

package/dist/seek-bzip/toHex.js

@@ -0,0 +1,36 @@
+"use strict";
+// from https://www.xaymar.com/articles/2020/12/08/fastest-uint8array-to-hex-string-conversion-in-javascript/
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.toHex = toHex;
+// Pre-Init
+const LUT_HEX_4b = [
+    '0',
+    '1',
+    '2',
+    '3',
+    '4',
+    '5',
+    '6',
+    '7',
+    '8',
+    '9',
+    'A',
+    'B',
+    'C',
+    'D',
+    'E',
+    'F',
+];
+const LUT_HEX_8b = new Array(0x100);
+for (let n = 0; n < 0x100; n++) {
+    LUT_HEX_8b[n] = `${LUT_HEX_4b[(n >>> 4) & 0xf]}${LUT_HEX_4b[n & 0xf]}`;
+}
+// End Pre-Init
+function toHex(buffer) {
+    let out = '';
+    for (let idx = 0, edx = buffer.length; idx < edx; idx++) {
+        out += LUT_HEX_8b[buffer[idx]];
+    }
+    return out;
+}
+//# sourceMappingURL=toHex.js.map

package/dist/seek-bzip/toHex.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"toHex.js","sourceRoot":"","sources":["../../src/seek-bzip/toHex.ts"],"names":[],"mappings":";AAAA,6GAA6G;;AA0B7G,sBAMC;AA9BD,WAAW;AACX,MAAM,UAAU,GAAG;IACjB,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;CACJ,CAAA;AACD,MAAM,UAAU,GAAG,IAAI,KAAK,CAAC,KAAK,CAAC,CAAA;AACnC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,EAAE,EAAE,CAAC;IAC/B,UAAU,CAAC,CAAC,CAAC,GAAG,GAAG,UAAU,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,UAAU,CAAC,CAAC,GAAG,GAAG,CAAC,EAAE,CAAA;AACxE,CAAC;AACD,eAAe;AACf,SAAgB,KAAK,CAAC,MAAkB;IACtC,IAAI,GAAG,GAAG,EAAE,CAAA;IACZ,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,MAAM,CAAC,MAAM,EAAE,GAAG,GAAG,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC;QACxD,GAAG,IAAI,UAAU,CAAC,MAAM,CAAC,GAAG,CAAE,CAAC,CAAA;IACjC,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}

package/esm/craiIndex.d.ts

@@ -1,4 +1,4 @@
-import { CramFileSource } from './cramFile/file';
+import { CramFileSource } from './cramFile/file.ts';
 export interface Slice {
     start: number;
     span: number;

package/esm/craiIndex.js

@@ -1,6 +1,6 @@
-import { CramMalformedError } from './errors';
-import { open } from './io';
-import { unzip } from './unzip';
+import { CramMalformedError } from "./errors.js";
+import { open } from "./io.js";
+import { unzip } from "./unzip.js";
 const BAI_MAGIC = 21_578_050; // BAI\1
 function addRecordToIndex(index, record) {
     const [seqId, start, span, containerStart, sliceStart, sliceBytes] = record;

package/esm/craiIndex.js.map

@@ -1 +1 @@
-{"version":3,"file":"craiIndex.js","sourceRoot":"","sources":["../src/craiIndex.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,kBAAkB,EAAE,MAAM,UAAU,CAAA;AAC7C,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAA;AAC3B,OAAO,EAAE,KAAK,EAAE,MAAM,SAAS,CAAA;AAI/B,MAAM,SAAS,GAAG,UAAU,CAAA,CAAC,QAAQ;AAYrC,SAAS,gBAAgB,CAAC,KAAkB,EAAE,MAAgB;IAC5D,MAAM,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,EAAE,cAAc,EAAE,UAAU,EAAE,UAAU,CAAC,GAAG,MAAM,CAAA;IAE3E,MAAM,CAAC,GAAG,KAAM,CAAA;IAChB,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC;QACd,KAAK,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;IACf,CAAC;IAED,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;QACZ,KAAK,EAAE,KAAM;QACb,IAAI,EAAE,IAAK;QACX,cAAc,EAAE,cAAe;QAC/B,UAAU,EAAE,UAAW;QACvB,UAAU,EAAE,UAAW;KACxB,CAAC,CAAA;AACJ,CAAC;AAED,SAAS,UAAU,CAAC,IAAgB;IAClC,OAAO,IAAI,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;AAC/D,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,SAAS;IAiB5B;;;;;;OAMG;IACH,YAAY,IAAoB;QAC9B,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,UAAU,CAAC,CAAA;IAC9D,CAAC;IAED,KAAK,CAAC,UAAU;QACd,MAAM,KAAK,GAAgB,EAAE,CAAA;QAC7B,MAAM,kBAAkB,GAAG,UAAU,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,EAAE,CAAC,CAAA;QACvE,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAA;QACxD,IACE,kBAAkB,CAAC,MAAM,GAAG,CAAC;YAC7B,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,SAAS,EACzC,CAAC;YACD,MAAM,IAAI,kBAAkB,CAC1B,+IAA+I,CAChJ,CAAA;QACH,CAAC;QACD,uEAAuE;QACvE,qEAAqE;QACrE,qEAAqE;QACrE,gBAAgB;QAChB,IAAI,aAAa,GAAa,EAAE,CAAA;QAChC,IAAI,aAAa,GAAG,EAAE,CAAA;QACtB,KAAK,MAAM,QAAQ,IAAI,kBAAkB,EAAE,CAAC;YAC1C,IACE,CAAC,QAAQ,IAAI,EAAE,IAAI,QAAQ,IAAI,EAAE,CAAC,CAAC,SAAS;gBAC5C,CAAC,CAAC,aAAa,IAAI,QAAQ,KAAK,EAAE,CAAC,CAAC,eAAe,EACnD,CAAC;gBACD,aAAa,IAAI,MAAM,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAA;YAChD,CAAC;iBAAM,IAAI,QAAQ,KAAK,CAAC,CAAC,QAAQ,EAAE,CAAC;gBACnC,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;gBACtD,aAAa,GAAG,EAAE,CAAA;YACpB,CAAC;iBAAM,IAAI,QAAQ,KAAK,EAAE,CAAC,QAAQ,EAAE,CAAC;gBACpC,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;gBACtD,aAAa,GAAG,EAAE,CAAA;gBAClB,gBAAgB,CAAC,KAAK,EAAE,aAAa,CAAC,CAAA;gBACtC,aAAa,GAAG,EAAE,CAAA;YACpB,CAAC;iBAAM,IAAI,QAAQ,KAAK,EAAE,CAAC,QAAQ,IAAI,QAAQ,KAAK,EAAE,CAAC,WAAW,EAAE,CAAC;gBACnE,oDAAoD;gBACpD,oCAAoC;gBACpC,MAAM,IAAI,kBAAkB,CAAC,0BAA0B,CAAC,CAAA;YAC1D,CAAC;QACH,CAAC;QAED,8DAA8D;QAC9D,IAAI,aAAa,EAAE,CAAC;YAClB,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;QACxD,CAAC;QACD,IAAI,aAAa,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC/B,gBAAgB,CAAC,KAAK,EAAE,aAAa,CAAC,CAAA;QACxC,CAAC;QAED,6BAA6B;QAC7B,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,EAAE;YAC7C,MAAM,EAAE,GAAG,GAAI,CAAA;YACf,KAAK,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,CAAC,CAAA;QACxE,CAAC,CAAC,CAAA;QACF,OAAO,KAAK,CAAA;IACd,CAAC;IAED,QAAQ;QACN,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE,CAAC;YACtB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACxD,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,2BAA2B,CAAC,KAAa;QAC7C,OAAO,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,CAAA;IACzC,CAAC;IAED;;;;;;;;;;OAUG;IACH,KAAK,CAAC,kBAAkB,CACtB,KAAa,EACb,UAAkB,EAClB,QAAgB;QAEhB,MAAM,UAAU,GAAG,CAAC,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,CAAA;QACjD,IAAI,CAAC,UAAU,EAAE,CAAC;YAChB,OAAO,EAAE,CAAA;QACX,CAAC;QAED,MAAM,OAAO,GAAG,CAAC,KAAY,EAAE,EAAE;YAC/B,MAAM,UAAU,GAAG,KAAK,CAAC,KAAK,CAAA;YAC9B,MAAM,QAAQ,GAAG,KAAK,CAAC,KAAK,GAAG,KAAK,CAAC,IAAI,CAAA;YACzC,IAAI,UAAU,GAAG,QAAQ,EAAE,CAAC;gBAC1B,OAAO,CAAC,CAAC,CAAA;YACX,CAAC,CAAC,0BAA0B;YAC5B,IAAI,QAAQ,IAAI,UAAU,EAAE,CAAC;gBAC3B,OAAO,CAAC,CAAA;YACV,CAAC,CAAC,wBAAwB;YAC1B,OAAO,CAAC,CAAA,CAAC,uBAAuB;QAClC,CAAC,CAAA;QACD,MAAM,IAAI,GAAG,EAAa,CAAA;QAC1B,KAAK,MAAM,KAAK,IAAI,UAAU,EAAE,CAAC;YAC/B,IAAI,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;gBACzB,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAClB,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;CACF"}
+{"version":3,"file":"craiIndex.js","sourceRoot":"","sources":["../src/craiIndex.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,kBAAkB,EAAE,MAAM,aAAa,CAAA;AAChD,OAAO,EAAE,IAAI,EAAE,MAAM,SAAS,CAAA;AAC9B,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAA;AAIlC,MAAM,SAAS,GAAG,UAAU,CAAA,CAAC,QAAQ;AAYrC,SAAS,gBAAgB,CAAC,KAAkB,EAAE,MAAgB;IAC5D,MAAM,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,EAAE,cAAc,EAAE,UAAU,EAAE,UAAU,CAAC,GAAG,MAAM,CAAA;IAE3E,MAAM,CAAC,GAAG,KAAM,CAAA;IAChB,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC;QACd,KAAK,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;IACf,CAAC;IAED,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;QACZ,KAAK,EAAE,KAAM;QACb,IAAI,EAAE,IAAK;QACX,cAAc,EAAE,cAAe;QAC/B,UAAU,EAAE,UAAW;QACvB,UAAU,EAAE,UAAW;KACxB,CAAC,CAAA;AACJ,CAAC;AAED,SAAS,UAAU,CAAC,IAAgB;IAClC,OAAO,IAAI,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;AAC/D,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,SAAS;IAiB5B;;;;;;OAMG;IACH,YAAY,IAAoB;QAC9B,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,UAAU,CAAC,CAAA;IAC9D,CAAC;IAED,KAAK,CAAC,UAAU;QACd,MAAM,KAAK,GAAgB,EAAE,CAAA;QAC7B,MAAM,kBAAkB,GAAG,UAAU,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,EAAE,CAAC,CAAA;QACvE,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAA;QACxD,IACE,kBAAkB,CAAC,MAAM,GAAG,CAAC;YAC7B,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,SAAS,EACzC,CAAC;YACD,MAAM,IAAI,kBAAkB,CAC1B,+IAA+I,CAChJ,CAAA;QACH,CAAC;QACD,uEAAuE;QACvE,qEAAqE;QACrE,qEAAqE;QACrE,gBAAgB;QAChB,IAAI,aAAa,GAAa,EAAE,CAAA;QAChC,IAAI,aAAa,GAAG,EAAE,CAAA;QACtB,KAAK,MAAM,QAAQ,IAAI,kBAAkB,EAAE,CAAC;YAC1C,IACE,CAAC,QAAQ,IAAI,EAAE,IAAI,QAAQ,IAAI,EAAE,CAAC,CAAC,SAAS;gBAC5C,CAAC,CAAC,aAAa,IAAI,QAAQ,KAAK,EAAE,CAAC,CAAC,eAAe,EACnD,CAAC;gBACD,aAAa,IAAI,MAAM,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAA;YAChD,CAAC;iBAAM,IAAI,QAAQ,KAAK,CAAC,CAAC,QAAQ,EAAE,CAAC;gBACnC,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;gBACtD,aAAa,GAAG,EAAE,CAAA;YACpB,CAAC;iBAAM,IAAI,QAAQ,KAAK,EAAE,CAAC,QAAQ,EAAE,CAAC;gBACpC,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;gBACtD,aAAa,GAAG,EAAE,CAAA;gBAClB,gBAAgB,CAAC,KAAK,EAAE,aAAa,CAAC,CAAA;gBACtC,aAAa,GAAG,EAAE,CAAA;YACpB,CAAC;iBAAM,IAAI,QAAQ,KAAK,EAAE,CAAC,QAAQ,IAAI,QAAQ,KAAK,EAAE,CAAC,WAAW,EAAE,CAAC;gBACnE,oDAAoD;gBACpD,oCAAoC;gBACpC,MAAM,IAAI,kBAAkB,CAAC,0BAA0B,CAAC,CAAA;YAC1D,CAAC;QACH,CAAC;QAED,8DAA8D;QAC9D,IAAI,aAAa,EAAE,CAAC;YAClB,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;QACxD,CAAC;QACD,IAAI,aAAa,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC/B,gBAAgB,CAAC,KAAK,EAAE,aAAa,CAAC,CAAA;QACxC,CAAC;QAED,6BAA6B;QAC7B,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,EAAE;YAC7C,MAAM,EAAE,GAAG,GAAI,CAAA;YACf,KAAK,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,CAAC,CAAA;QACxE,CAAC,CAAC,CAAA;QACF,OAAO,KAAK,CAAA;IACd,CAAC;IAED,QAAQ;QACN,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE,CAAC;YACtB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACxD,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,2BAA2B,CAAC,KAAa;QAC7C,OAAO,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,CAAA;IACzC,CAAC;IAED;;;;;;;;;;OAUG;IACH,KAAK,CAAC,kBAAkB,CACtB,KAAa,EACb,UAAkB,EAClB,QAAgB;QAEhB,MAAM,UAAU,GAAG,CAAC,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,CAAA;QACjD,IAAI,CAAC,UAAU,EAAE,CAAC;YAChB,OAAO,EAAE,CAAA;QACX,CAAC;QAED,MAAM,OAAO,GAAG,CAAC,KAAY,EAAE,EAAE;YAC/B,MAAM,UAAU,GAAG,KAAK,CAAC,KAAK,CAAA;YAC9B,MAAM,QAAQ,GAAG,KAAK,CAAC,KAAK,GAAG,KAAK,CAAC,IAAI,CAAA;YACzC,IAAI,UAAU,GAAG,QAAQ,EAAE,CAAC;gBAC1B,OAAO,CAAC,CAAC,CAAA;YACX,CAAC,CAAC,0BAA0B;YAC5B,IAAI,QAAQ,IAAI,UAAU,EAAE,CAAC;gBAC3B,OAAO,CAAC,CAAA;YACV,CAAC,CAAC,wBAAwB;YAC1B,OAAO,CAAC,CAAA,CAAC,uBAAuB;QAClC,CAAC,CAAA;QACD,MAAM,IAAI,GAAG,EAAa,CAAA;QAC1B,KAAK,MAAM,KAAK,IAAI,UAAU,EAAE,CAAC;YAC/B,IAAI,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;gBACzB,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAClB,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;CACF"}

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

@@ -1,6 +1,6 @@
-import { CramFileBlock } from '../file';
-import CramSlice from '../slice';
-import { DataType } from './dataSeriesTypes';
+import { CramFileBlock } from '../file.ts';
+import { DataType } from './dataSeriesTypes.ts';
+import CramSlice from '../slice/index.ts';
 export interface DataTypeMapping {
     byte: number;
     int: number;

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

@@ -1,8 +1,8 @@
-import CramCodec, { Cursors } from './_base';
-import { BetaEncoding } from '../encoding';
-import { CramFileBlock } from '../file';
-import CramSlice from '../slice';
+import CramCodec, { Cursors } from './_base.ts';
+import { BetaEncoding } from '../encoding.ts';
+import { CramFileBlock } from '../file.ts';
+import CramSlice from '../slice/index.ts';
 export default class BetaCodec extends CramCodec<'int', BetaEncoding['parameters']> {
     constructor(parameters: BetaEncoding['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/beta.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 BetaCodec extends CramCodec {
     constructor(parameters, dataType) {
         super(parameters, dataType);
@@ -8,7 +8,7 @@ export default class BetaCodec extends CramCodec {
             throw new CramUnimplementedError(`${this.dataType} decoding not yet implemented by BETA codec`);
         }
     }
-    decode(slice, coreDataBlock, blocksByContentId, cursors) {
+    decode(_slice, coreDataBlock, _blocksByContentId, cursors) {
         const fromBits = getBits(coreDataBlock.content, cursors.coreBlock, this.parameters.length);
         return fromBits - this.parameters.offset;
     }

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

@@ -1 +1 @@
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package/esm/cramFile/codecs/byteArrayLength.d.ts

@@ -1,8 +1,8 @@
-import CramCodec, { Cursors } from './_base';
-import { ByteArrayLengthEncoding, CramEncoding } from '../encoding';
-import { CramFileBlock } from '../file';
-import CramSlice from '../slice';
-import { DataType } from './dataSeriesTypes';
+import CramCodec, { Cursors } from './_base.ts';
+import { ByteArrayLengthEncoding, CramEncoding } from '../encoding.ts';
+import { CramFileBlock } from '../file.ts';
+import { DataType } from './dataSeriesTypes.ts';
+import CramSlice from '../slice/index.ts';
 type CramCodecFactory = <TData extends DataType = DataType>(encodingData: CramEncoding, dataType: TData | 'ignore') => CramCodec<TData>;
 export default class ByteArrayStopCodec extends CramCodec<'byteArray', ByteArrayLengthEncoding['parameters']> {
     private instantiateCodec;

package/esm/cramFile/codecs/byteArrayLength.js

@@ -1,5 +1,5 @@
-import CramCodec from './_base';
-import { tinyMemoize } from '../util';
+import CramCodec from "./_base.js";
+import { tinyMemoize } from "../util.js";
 export default class ByteArrayStopCodec extends CramCodec {
     constructor(parameters, dataType, instantiateCodec) {
         super(parameters, dataType);

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

@@ -1 +1 @@
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package/esm/cramFile/codecs/byteArrayStop.d.ts

@@ -1,8 +1,8 @@
-import CramCodec, { Cursor, Cursors } from './_base';
-import { ByteArrayStopCramEncoding } from '../encoding';
-import { CramFileBlock } from '../file';
-import CramSlice from '../slice';
+import CramCodec, { Cursor, Cursors } from './_base.ts';
+import { ByteArrayStopCramEncoding } from '../encoding.ts';
+import { CramFileBlock } from '../file.ts';
+import CramSlice from '../slice/index.ts';
 export default class ByteArrayStopCodec extends CramCodec<'byteArray', ByteArrayStopCramEncoding['parameters']> {
-    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): Uint8Array<ArrayBufferLike>;
+    decode(_slice: CramSlice, _coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): Uint8Array<ArrayBufferLike>;
     _decodeByteArray(contentBlock: CramFileBlock, cursor: Cursor): Uint8Array<ArrayBufferLike>;
 }

package/esm/cramFile/codecs/byteArrayStop.js

@@ -1,8 +1,8 @@
-import CramCodec from './_base';
-import { CramMalformedError } from '../../errors';
-import { CramBufferOverrunError } from './getBits';
+import CramCodec from "./_base.js";
+import { CramMalformedError } from "../../errors.js";
+import { CramBufferOverrunError } from "./getBits.js";
 export default class ByteArrayStopCodec extends CramCodec {
-    decode(slice, coreDataBlock, blocksByContentId, cursors) {
+    decode(_slice, _coreDataBlock, blocksByContentId, cursors) {
         const { blockContentId } = this.parameters;
         const contentBlock = blocksByContentId[blockContentId];
         if (!contentBlock) {

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

@@ -1 +1 @@
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package/esm/cramFile/codecs/dataSeriesTypes.d.ts

@@ -1,4 +1,4 @@
-import { CramEncoding } from '../encoding';
+import { CramEncoding } from '../encoding.ts';
 export type DataType = 'int' | 'byte' | 'long' | 'byteArray';
 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';
 export type DataSeriesEncodingMap = Record<DataSeriesEncodingKey, CramEncoding>;

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

@@ -1,11 +1,11 @@
-import CramCodec, { Cursor, Cursors } from './_base';
-import { CramFileBlock } from '../file';
-import CramSlice from '../slice';
-import { ExternalCramEncoding } from '../encoding';
+import CramCodec, { Cursor, Cursors } from './_base.ts';
+import { CramFileBlock } from '../file.ts';
+import CramSlice from '../slice/index.ts';
+import { ExternalCramEncoding } from '../encoding.ts';
 export default class ExternalCodec extends CramCodec<'int' | 'byte', ExternalCramEncoding['parameters']> {
     private readonly _decodeData;
     constructor(parameters: ExternalCramEncoding['parameters'], dataType: 'int' | 'byte');
-    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number | undefined;
+    decode(_slice: CramSlice, _coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number | undefined;
     _decodeInt(contentBlock: CramFileBlock, cursor: Cursor): number;
     _decodeByte(contentBlock: CramFileBlock, cursor: Cursor): number;
 }

package/esm/cramFile/codecs/external.js

@@ -1,7 +1,7 @@
-import CramCodec from './_base';
-import { CramUnimplementedError } from '../../errors';
-import { parseItf8 } from '../util';
-import { CramBufferOverrunError } from './getBits';
+import CramCodec from "./_base.js";
+import { CramUnimplementedError } from "../../errors.js";
+import { parseItf8 } from "../util.js";
+import { CramBufferOverrunError } from "./getBits.js";
 export default class ExternalCodec extends CramCodec {
     constructor(parameters, dataType) {
         super(parameters, dataType);
@@ -15,11 +15,12 @@ export default class ExternalCodec extends CramCodec {
             throw new CramUnimplementedError(`${this.dataType} decoding not yet implemented by EXTERNAL codec`);
         }
     }
-    decode(slice, coreDataBlock, blocksByContentId, cursors) {
+    decode(_slice, _coreDataBlock, blocksByContentId, cursors) {
         const { blockContentId } = this.parameters;
         const contentBlock = blocksByContentId[blockContentId];
-        const cursor = cursors.externalBlocks.getCursor(blockContentId);
-        return contentBlock ? this._decodeData(contentBlock, cursor) : undefined;
+        return contentBlock
+            ? this._decodeData(contentBlock, cursors.externalBlocks.getCursor(blockContentId))
+            : undefined;
     }
     _decodeInt(contentBlock, cursor) {
         const [result, bytesRead] = parseItf8(contentBlock.content, cursor.bytePosition);

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

@@ -1 +1 @@
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+{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":"AAAA,OAAO,SAA8B,MAAM,YAAY,CAAA;AACvD,OAAO,EAAE,sBAAsB,EAAE,MAAM,iBAAiB,CAAA;AAGxD,OAAO,EAAE,SAAS,EAAE,MAAM,YAAY,CAAA;AACtC,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AAGrD,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,SAG1C;IAMC,YACE,UAA8C,EAC9C,QAAwB;QAExB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,UAAU,CAAA;QACpC,CAAC;aAAM,IAAI,IAAI,CAAC,QAAQ,KAAK,MAAM,EAAE,CAAC;YACpC,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,CAAA;QACrC,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,sBAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,iDAAiD,CAClE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,MAAiB,EACjB,cAA6B,EAC7B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,EAAE,cAAc,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QAC1C,MAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QACtD,OAAO,YAAY;YACjB,CAAC,CAAC,IAAI,CAAC,WAAW,CACd,YAAY,EACZ,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CACjD;YACH,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,UAAU,CAAC,YAA2B,EAAE,MAAc;QACpD,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,SAAS,CACnC,YAAY,CAAC,OAAO,EACpB,MAAM,CAAC,YAAY,CACpB,CAAA;QACD,MAAM,CAAC,YAAY,GAAG,MAAM,CAAC,YAAY,GAAG,SAAS,CAAA;QACrD,OAAO,MAAM,CAAA;IACf,CAAC;IAED,WAAW,CAAC,YAA2B,EAAE,MAAc;QACrD,IAAI,MAAM,CAAC,YAAY,IAAI,YAAY,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC;YACvD,MAAM,IAAI,sBAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAE,CAAA;IACrD,CAAC;CACF"}

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

@@ -1,8 +1,8 @@
-import CramCodec, { Cursors } from './_base';
-import { GammaEncoding } from '../encoding';
-import { CramFileBlock } from '../file';
-import CramSlice from '../slice';
+import CramCodec, { Cursors } from './_base.ts';
+import { GammaEncoding } from '../encoding.ts';
+import { CramFileBlock } from '../file.ts';
+import CramSlice from '../slice/index.ts';
 export default class GammaCodec extends CramCodec<'int', GammaEncoding['parameters']> {
     constructor(parameters: GammaEncoding['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/gamma.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 GammaCodec extends CramCodec {
     constructor(parameters, dataType) {
         super(parameters, dataType);
@@ -8,7 +8,7 @@ export default class GammaCodec extends CramCodec {
             throw new CramUnimplementedError(`${this.dataType} decoding not yet implemented by GAMMA codec`);
         }
     }
-    decode(slice, coreDataBlock, blocksByContentId, cursors) {
+    decode(_slice, coreDataBlock, _blocksByContentId, cursors) {
         let length = 1;
         while (getBits(coreDataBlock.content, cursors.coreBlock, 1) === 0) {
             length = length + 1;

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

@@ -1 +1 @@
-{"version":3,"file":"gamma.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/gamma.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,UAAW,SAAQ,SAGvC;IACC,YAAY,UAAuC,EAAE,QAAe;QAClE,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,8CAA8C,CAC/D,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,IAAI,MAAM,GAAG,CAAC,CAAA;QAEd,OAAO,OAAO,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;YAClE,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;QACrB,CAAC;QAED,MAAM,QAAQ,GAAG,OAAO,CACtB,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,MAAM,GAAG,CAAC,CACX,CAAA;QAED,MAAM,KAAK,GAAG,QAAQ,GAAG,CAAC,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA;QAC5C,OAAO,KAAK,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACvC,CAAC;CACF"}
+{"version":3,"file":"gamma.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/gamma.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,UAAW,SAAQ,SAGvC;IACC,YAAY,UAAuC,EAAE,QAAe;QAClE,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,8CAA8C,CAC/D,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,MAAiB,EACjB,aAA4B,EAC5B,kBAAiD,EACjD,OAAgB;QAEhB,IAAI,MAAM,GAAG,CAAC,CAAA;QAEd,OAAO,OAAO,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;YAClE,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;QACrB,CAAC;QAED,MAAM,QAAQ,GAAG,OAAO,CACtB,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,MAAM,GAAG,CAAC,CACX,CAAA;QAED,MAAM,KAAK,GAAG,QAAQ,GAAG,CAAC,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA;QAC5C,OAAO,KAAK,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACvC,CAAC;CACF"}

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

@@ -1,7 +1,7 @@
-import CramCodec, { Cursor, Cursors } from './_base';
-import { HuffmanEncoding } from '../encoding';
-import { CramFileBlock } from '../file';
-import CramSlice from '../slice';
+import CramCodec, { Cursor, Cursors } from './_base.ts';
+import { HuffmanEncoding } from '../encoding.ts';
+import { CramFileBlock } from '../file.ts';
+import CramSlice from '../slice/index.ts';
 export default class HuffmanIntCodec extends CramCodec<'byte' | 'int', HuffmanEncoding['parameters']> {
     private codes;
     private codeBook;
@@ -14,7 +14,7 @@ export default class HuffmanIntCodec extends CramCodec<'byte' | 'int', HuffmanEn
     buildCodeBook(): void;
     buildCodes(): void;
     buildCaches(): void;
-    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number;
+    decode(slice: CramSlice, coreDataBlock: CramFileBlock, _blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number;
     _decodeZeroLengthCode(): number;
-    _decode(slice: CramSlice, coreDataBlock: CramFileBlock, coreCursor: Cursor): number;
+    _decode(_slice: CramSlice, coreDataBlock: CramFileBlock, coreCursor: Cursor): number;
 }

package/esm/cramFile/codecs/huffman.js

@@ -1,6 +1,6 @@
-import CramCodec from './_base';
-import { getBits } from './getBits';
-import { CramMalformedError } from '../../errors';
+import CramCodec from "./_base.js";
+import { getBits } from "./getBits.js";
+import { CramMalformedError } from "../../errors.js";
 function numberOfSetBits(ii) {
     let i = (ii - (ii >> 1)) & 0x55555555;
     i = (i & 0x33333333) + ((i >> 2) & 0x33333333);
@@ -82,7 +82,7 @@ export default class HuffmanIntCodec extends CramCodec {
             this.bitCodeToValue[this.sortedCodes[i].bitCode] = i;
         }
     }
-    decode(slice, coreDataBlock, blocksByContentId, cursors) {
+    decode(slice, coreDataBlock, _blocksByContentId, cursors) {
         return this._decode(slice, coreDataBlock, cursors.coreBlock);
     }
     // _decodeNull() {
@@ -92,7 +92,7 @@ export default class HuffmanIntCodec extends CramCodec {
     _decodeZeroLengthCode() {
         return this.sortedCodes[0].value;
     }
-    _decode(slice, coreDataBlock, coreCursor) {
+    _decode(_slice, coreDataBlock, coreCursor) {
         const input = coreDataBlock.content;
         let prevLen = 0;
         let bits = 0;

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

@@ -1 +1 @@
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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 @@
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+{"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;