npm - @gmod/cram - Versions diffs - 5.0.5 → 5.0.6 - Mend

@gmod/cram 5.0.5 → 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 (34) hide show

package/README.md +0 -4
package/dist/cram-bundle.js +1 -1
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/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 +9 -9
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/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;
         }

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

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

@@ -1,4 +1,5 @@
-import { inflate } from 'pako';
+import * as pkg from 'pako';
+const { inflate } = pkg;
 export function unzip(input) {
     return inflate(input);
 }

package/esm/unzip.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,~~MAAM~~,~~MAAM~~,CAAA;~~AAE9B~~,MAAM,UAAU,KAAK,CAAC,KAAiB;IACrC,OAAO,OAAO,CAAC,KAAK,CAAC,CAAA;AACvB,CAAC"}
1	+ {"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,GAAG,MAAM,MAAM,CAAA;AAC3B,MAAM,EAAE,OAAO,EAAE,GAAG,GAAG,CAAA;AAEvB,MAAM,UAAU,KAAK,CAAC,KAAiB;IACrC,OAAO,OAAO,CAAC,KAAK,CAAC,CAAA;AACvB,CAAC"}

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/cram",
-  "version": "5.0.5",
+  "version": "5.0.6",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",
@@ -50,29 +50,29 @@
   ],
   "dependencies": {
     "crc": "^4.3.2",
-    "generic-filehandle2": "^2.0.1",
+    "generic-filehandle2": "^2.0.12",
     "md5": "^2.2.1",
     "pako": "^1.0.4",
     "quick-lru": "^4.0.1",
     "xz-decompress": "^0.2.1"
   },
   "devDependencies": {
-    "@gmod/indexedfasta": "^4.0.1",
+    "@gmod/indexedfasta": "^4.0.6",
     "@types/md5": "^2.3.2",
     "@types/pako": "^1.0.3",
-    "@vitest/coverage-v8": "^3.0.1",
+    "@vitest/coverage-v8": "^3.2.3",
     "buffer": "^6.0.3",
     "documentation": "^14.0.3",
-    "eslint": "^9.9.0",
+    "eslint": "^9.29.0",
     "eslint-plugin-import": "^2.31.0",
-    "eslint-plugin-unicorn": "^59.0.0",
+    "eslint-plugin-unicorn": "^60.0.0",
     "mock-fs": "^5.2.0",
     "prettier": "^3.2.5",
     "rimraf": "^6.0.1",
     "typescript": "^5.7.0",
-    "typescript-eslint": "^8.31.1",
-    "vitest": "^3.0.1",
-    "webpack": "^5.99.7",
+    "typescript-eslint": "^8.34.0",
+    "vitest": "^3.2.3",
+    "webpack": "^5.99.9",
     "webpack-cli": "^6.0.1"
   },
   "publishConfig": {

package/src/cramFile/container/compressionScheme.ts CHANGED Viewed

@@ -100,6 +100,7 @@ export default class CramContainerCompressionScheme {
     // interpret some of the preservation map tags for convenient use
     this.readNamesIncluded = content.preservation.RN
     this.APdelta = content.preservation.AP
     this.referenceRequired = !!content.preservation.RR
     this.tagIdsDictionary = content.preservation.TD
     this.substitutionMatrix = parseSubstitutionMatrix(content.preservation.SM)

package/src/cramFile/file.ts CHANGED Viewed

@@ -110,12 +110,15 @@ 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`,
       )
+    } else {
+      return definition
     }
-    return definition
   }
   // memoize

package/src/cramFile/sectionParsers.ts CHANGED Viewed

@@ -166,7 +166,7 @@ export interface CramPreservationMap {
   PI: boolean
   RN: boolean
   AP: boolean
-  RR: boolean
+  RR: boolean | undefined
   SM: [number, number, number, number, number]
   TD: CramTagDictionary
 }

package/src/htscodecs/rans.ts CHANGED Viewed

@@ -95,7 +95,7 @@ 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?
@@ -163,7 +163,7 @@ 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/src/htscodecs/rans4x16.ts CHANGED Viewed

@@ -320,7 +320,7 @@ function ReadAlphabet(src) {
   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?
@@ -403,7 +403,7 @@ 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/src/seek-bzip/index.ts CHANGED Viewed

@@ -271,7 +271,7 @@ 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
@@ -304,7 +304,7 @@ 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/src/unzip.ts CHANGED Viewed

@@ -1,4 +1,5 @@
-import { inflate } from 'pako'
+import * as pkg from 'pako'
+const { inflate } = pkg
 export function unzip(input: Uint8Array) {
   return inflate(input)