npm - @gmod/cram - Versions diffs - 5.0.4 → 5.0.6 - Mend

@gmod/cram 5.0.4 → 5.0.6

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (36) hide show

package/README.md +0 -4
package/dist/cram-bundle.js +2 -1
package/dist/cram-bundle.js.LICENSE.txt +12 -0
package/dist/cramFile/container/compressionScheme.js.map +1 -1
package/dist/cramFile/file.js +7 -2
package/dist/cramFile/file.js.map +1 -1
package/dist/cramFile/sectionParsers.d.ts +1 -1
package/dist/htscodecs/rans.js +2 -2
package/dist/htscodecs/rans.js.map +1 -1
package/dist/htscodecs/rans4x16.js +2 -2
package/dist/htscodecs/rans4x16.js.map +1 -1
package/dist/package.json +1 -0
package/dist/seek-bzip/index.js +2 -2
package/dist/seek-bzip/index.js.map +1 -1
package/dist/unzip.js +36 -2
package/dist/unzip.js.map +1 -1
package/esm/cramFile/container/compressionScheme.js.map +1 -1
package/esm/cramFile/file.js +7 -2
package/esm/cramFile/file.js.map +1 -1
package/esm/cramFile/sectionParsers.d.ts +1 -1
package/esm/htscodecs/rans.js +2 -2
package/esm/htscodecs/rans.js.map +1 -1
package/esm/htscodecs/rans4x16.js +2 -2
package/esm/htscodecs/rans4x16.js.map +1 -1
package/esm/seek-bzip/index.js +2 -2
package/esm/seek-bzip/index.js.map +1 -1
package/esm/unzip.js +2 -1
package/esm/unzip.js.map +1 -1
package/package.json +10 -13
package/src/cramFile/container/compressionScheme.ts +1 -0
package/src/cramFile/file.ts +5 -2
package/src/cramFile/sectionParsers.ts +1 -1
package/src/htscodecs/rans.ts +2 -2
package/src/htscodecs/rans4x16.ts +2 -2
package/src/seek-bzip/index.ts +2 -2
package/src/unzip.ts +2 -1

package/dist/htscodecs/rans.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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package/dist/htscodecs/rans4x16.js CHANGED Viewed

@@ -277,7 +277,7 @@ function ReadAlphabet(src) {
     } while (sym != 0);
     return A;
 }
-// Decode a single table of order-0 frequences,
+// Decode a single table of order-0 frequencies,
 // filling out the F and C arrays.
 function ReadFrequencies0(src, F, C) {
     // Initialise; not in the specification - implicit?
@@ -345,7 +345,7 @@ function NormaliseFrequencies0_Shift(F, bits) {
 }
 // ----------------------------------------------------------------------
 // Order-1 decoder
-// Decode a table of order-1 frequences,
+// Decode a table of order-1 frequencies,
 // filling out the F and C arrays.
 function ReadFrequencies1(src, F, C, shift) {
     // Initialise; not in the specification - implicit?

package/dist/htscodecs/rans4x16.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/package.json ADDED Viewed

	@@ -0,0 +1 @@
1	+ {"type": "commonjs"}

package/dist/seek-bzip/index.js CHANGED Viewed

@@ -256,7 +256,7 @@ class Bunzip {
             hufGroup.base = new Uint32Array(MAX_HUFCODE_BITS + 1);
             hufGroup.minLen = minLen;
             hufGroup.maxLen = maxLen;
-            /* Calculate permute[].  Concurently, initialize temp[] and limit[]. */
+            /* Calculate permute[].  Concurrently, initialize temp[] and limit[]. */
             let pp = 0;
             for (i = minLen; i <= maxLen; i++) {
                 temp[i] = hufGroup.limit[i] = 0;
@@ -289,7 +289,7 @@ class Bunzip {
                 hufGroup.base[i + 1] = pp - t;
             }
             hufGroup.limit[maxLen + 1] =
-                Number.MAX_VALUE; /* Sentinal value for reading next sym. */
+                Number.MAX_VALUE; /* Sentinel value for reading next sym. */
             hufGroup.limit[maxLen] = pp + temp[maxLen] - 1;
             hufGroup.base[minLen] = 0;
         }

package/dist/seek-bzip/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/unzip.js CHANGED Viewed

@@ -1,8 +1,42 @@
 "use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.unzip = unzip;
-const pako_1 = require("pako");
+const pkg = __importStar(require("pako"));
+const { inflate } = pkg;
 function unzip(input) {
-    return (0, pako_1.inflate)(input);
+    return inflate(input);
 }
 //# sourceMappingURL=unzip.js.map

package/dist/unzip.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":"~~;;AAEA~~,sBAEC;~~AAJD,+BAA8B~~;~~AAE9B~~,SAAgB,KAAK,CAAC,KAAiB;IACrC,OAAO,~~IAAA~~,~~cAAO~~,~~EAAC,~~KAAK,CAAC,CAAA;AACvB,CAAC"}
1	+ {"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAGA,sBAEC;AALD,0CAA2B;AAC3B,MAAM,EAAE,OAAO,EAAE,GAAG,GAAG,CAAA;AAEvB,SAAgB,KAAK,CAAC,KAAiB;IACrC,OAAO,OAAO,CAAC,KAAK,CAAC,CAAA;AACvB,CAAC"}

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

	@@ -1 +1 @@
1	- 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1	+ {"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;QAEtC,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,O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package/esm/cramFile/file.js CHANGED Viewed

@@ -60,10 +60,15 @@ export default class CramFile {
         const { maxLength, parser } = cramFileDefinition();
         const headbytes = await this.file.read(maxLength, 0);
         const definition = parser(headbytes).value;
-        if (definition.majorVersion !== 2 && definition.majorVersion !== 3) {
+        if (definition.magic !== 'CRAM') {
+            throw new Error('Not a CRAM file, does not match magic string');
+        }
+        else if (definition.majorVersion !== 2 && definition.majorVersion !== 3) {
             throw new CramUnimplementedError(`CRAM version ${definition.majorVersion} not supported`);
         }
-        return definition;
+        else {
+            return definition;
+        }
     }
     // memoize
     async getSamHeader() {

package/esm/cramFile/file.js.map CHANGED Viewed

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

@@ -51,7 +51,7 @@ export interface CramPreservationMap {
     PI: boolean;
     RN: boolean;
     AP: boolean;
-    RR: boolean;
+    RR: boolean | undefined;
     SM: [number, number, number, number, number];
     TD: CramTagDictionary;
 }

package/esm/htscodecs/rans.js CHANGED Viewed

@@ -82,7 +82,7 @@ export function decode(src) {
 }
 // ----------------------------------------------------------------------
 // Order-0 decoder
-// Decode a single table of order-0 frequences,
+// Decode a single table of order-0 frequencies,
 // filling out the F and C arrays.
 function ReadFrequencies0(src, F, C) {
     // Initialise; not in the specification - implicit?
@@ -140,7 +140,7 @@ function RansDecode0(src, nbytes) {
 }
 // ----------------------------------------------------------------------
 // Order-1 decoder
-// Decode a table of order-1 frequences,
+// Decode a table of order-1 frequencies,
 // filling out the F and C arrays.
 function ReadFrequencies1(src, F, C) {
     // Initialise; not in the specification - implicit?

package/esm/htscodecs/rans.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/htscodecs/rans4x16.js CHANGED Viewed

@@ -271,7 +271,7 @@ function ReadAlphabet(src) {
     } while (sym != 0);
     return A;
 }
-// Decode a single table of order-0 frequences,
+// Decode a single table of order-0 frequencies,
 // filling out the F and C arrays.
 function ReadFrequencies0(src, F, C) {
     // Initialise; not in the specification - implicit?
@@ -339,7 +339,7 @@ function NormaliseFrequencies0_Shift(F, bits) {
 }
 // ----------------------------------------------------------------------
 // Order-1 decoder
-// Decode a table of order-1 frequences,
+// Decode a table of order-1 frequencies,
 // filling out the F and C arrays.
 function ReadFrequencies1(src, F, C, shift) {
     // Initialise; not in the specification - implicit?

package/esm/htscodecs/rans4x16.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/seek-bzip/index.js CHANGED Viewed

@@ -250,7 +250,7 @@ class Bunzip {
             hufGroup.base = new Uint32Array(MAX_HUFCODE_BITS + 1);
             hufGroup.minLen = minLen;
             hufGroup.maxLen = maxLen;
-            /* Calculate permute[].  Concurently, initialize temp[] and limit[]. */
+            /* Calculate permute[].  Concurrently, initialize temp[] and limit[]. */
             let pp = 0;
             for (i = minLen; i <= maxLen; i++) {
                 temp[i] = hufGroup.limit[i] = 0;
@@ -283,7 +283,7 @@ class Bunzip {
                 hufGroup.base[i + 1] = pp - t;
             }
             hufGroup.limit[maxLen + 1] =
-                Number.MAX_VALUE; /* Sentinal value for reading next sym. */
+                Number.MAX_VALUE; /* Sentinel value for reading next sym. */
             hufGroup.limit[maxLen] = pp + temp[maxLen] - 1;
             hufGroup.base[minLen] = 0;
         }