npm - @gmod/cram - Versions diffs - 2.0.0 → 2.0.1 - Mend

@gmod/cram 2.0.0 → 2.0.1

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 (73) hide show

package/dist/craiIndex.js.map +1 -1
package/dist/cram-bundle.js +1 -1
package/dist/cramFile/codecs/beta.js.map +1 -1
package/dist/cramFile/codecs/byteArrayLength.js.map +1 -1
package/dist/cramFile/codecs/byteArrayStop.js.map +1 -1
package/dist/cramFile/codecs/external.js.map +1 -1
package/dist/cramFile/codecs/gamma.js.map +1 -1
package/dist/cramFile/codecs/getBits.js.map +1 -1
package/dist/cramFile/codecs/huffman.js.map +1 -1
package/dist/cramFile/codecs/index.js.map +1 -1
package/dist/cramFile/codecs/subexp.js.map +1 -1
package/dist/cramFile/container/compressionScheme.js.map +1 -1
package/dist/cramFile/container/index.js.map +1 -1
package/dist/cramFile/file.d.ts +8 -1
package/dist/cramFile/file.js.map +1 -1
package/dist/cramFile/record.js.map +1 -1
package/dist/cramFile/sectionParsers.d.ts +1 -0
package/dist/cramFile/sectionParsers.js +7 -7
package/dist/cramFile/sectionParsers.js.map +1 -1
package/dist/cramFile/slice/decodeRecord.js +1 -1
package/dist/cramFile/slice/decodeRecord.js.map +1 -1
package/dist/cramFile/slice/index.js.map +1 -1
package/dist/cramFile/util.d.ts +1 -0
package/dist/cramFile/util.js.map +1 -1
package/dist/indexedCramFile.js.map +1 -1
package/dist/io/index.js.map +1 -1
package/dist/rans/d04.js.map +1 -1
package/dist/rans/d14.js.map +1 -1
package/dist/rans/decoding.js.map +1 -1
package/dist/rans/frequencies.js.map +1 -1
package/dist/rans/index.js.map +1 -1
package/dist/sam.d.ts +5 -6
package/dist/sam.js +23 -7
package/dist/sam.js.map +1 -1
package/dist/typescript.js.map +1 -1
package/dist/unzip.d.ts +1 -0
package/esm/craiIndex.js.map +1 -1
package/esm/cramFile/codecs/beta.js.map +1 -1
package/esm/cramFile/codecs/byteArrayLength.js.map +1 -1
package/esm/cramFile/codecs/byteArrayStop.js.map +1 -1
package/esm/cramFile/codecs/external.js.map +1 -1
package/esm/cramFile/codecs/gamma.js.map +1 -1
package/esm/cramFile/codecs/getBits.js.map +1 -1
package/esm/cramFile/codecs/huffman.js.map +1 -1
package/esm/cramFile/codecs/index.js.map +1 -1
package/esm/cramFile/codecs/subexp.js.map +1 -1
package/esm/cramFile/container/compressionScheme.js.map +1 -1
package/esm/cramFile/container/index.js.map +1 -1
package/esm/cramFile/file.d.ts +8 -1
package/esm/cramFile/file.js.map +1 -1
package/esm/cramFile/record.js.map +1 -1
package/esm/cramFile/sectionParsers.d.ts +1 -0
package/esm/cramFile/sectionParsers.js +7 -7
package/esm/cramFile/sectionParsers.js.map +1 -1
package/esm/cramFile/slice/decodeRecord.js +1 -1
package/esm/cramFile/slice/decodeRecord.js.map +1 -1
package/esm/cramFile/slice/index.js.map +1 -1
package/esm/cramFile/util.d.ts +1 -0
package/esm/cramFile/util.js.map +1 -1
package/esm/indexedCramFile.js.map +1 -1
package/esm/io/index.js.map +1 -1
package/esm/rans/d04.js.map +1 -1
package/esm/rans/d14.js.map +1 -1
package/esm/rans/decoding.js.map +1 -1
package/esm/rans/frequencies.js.map +1 -1
package/esm/rans/index.js.map +1 -1
package/esm/sam.d.ts +5 -6
package/esm/sam.js +23 -7
package/esm/sam.js.map +1 -1
package/esm/typescript.js.map +1 -1
package/esm/unzip.d.ts +1 -0
package/package.json +2 -2
package/src/sam.ts +30 -14

package/esm/cramFile/slice/decodeRecord.js CHANGED Viewed

@@ -135,7 +135,7 @@ function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries,
         // map of operator name -> data series name
         const data1Schema = {
             B: ['character', 'BA'],
-            S: ['string', majorVersion > 1 ? 'SC' : 'IN'],
+            S: ['string', majorVersion > 1 ? 'SC' : 'IN'], // IN if cram v1, SC otherwise
             X: ['number', 'BS'],
             D: ['number', 'DL'],
             I: ['string', 'IN'],

package/esm/cramFile/slice/decodeRecord.js.map CHANGED Viewed

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

@@ -1,3 +1,4 @@
+/// <reference path="../../src/typings/binary-parser.d.ts" />
 /// <reference types="node" />
 import { Parser } from '@gmod/binary-parser';
 export declare function itf8Size(v: number): 1 | 2 | 3 | 4 | 5;

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

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

@@ -1,8 +1,7 @@
-export type HeaderDataItem = {
+export declare function parseHeaderText(text: string): {
     tag: string;
-    data: Array<{
+    data: {
         tag: string;
-        value: string;
-    }>;
-};
-export declare function parseHeaderText(text: string): HeaderDataItem[];
+        value: string | undefined;
+    }[];
+}[];

package/esm/sam.js CHANGED Viewed

@@ -1,16 +1,32 @@
 export function parseHeaderText(text) {
     const lines = text.split(/\r?\n/);
     const data = [];
-    lines.forEach(line => {
+    for (const line of lines) {
         const [tag, ...fields] = line.split(/\t/);
-        const parsedFields = fields.map(f => {
-            const [fieldTag, value] = f.split(':', 2);
-            return { tag: fieldTag, value };
-        });
         if (tag) {
-            data.push({ tag: tag.substr(1), data: parsedFields });
+            data.push({
+                tag: tag.slice(1),
+                data: fields.map(f => {
+                    const r = f.indexOf(':');
+                    if (r !== -1) {
+                        return {
+                            tag: f.slice(0, r),
+                            value: f.slice(r + 1),
+                        };
+                    }
+                    else {
+                        // @CO lines are not comma separated.
+                        // See "samtools view -H c2\#pad.3.0.cram"
+                        // so, just store value tag itself
+                        return {
+                            tag: f,
+                            value: undefined,
+                        };
+                    }
+                }),
+            });
         }
-    });
+    }
     return data;
 }
 //# sourceMappingURL=sam.js.map

package/esm/sam.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/typescript.js.map CHANGED Viewed

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package/esm/unzip.d.ts CHANGED Viewed

@@ -1,2 +1,3 @@
+/// <reference types="node" />
 import { gunzipSync } from 'zlib';
 export { gunzipSync as unzip };

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/cram",
-  "version": "2.0.0",
+  "version": "2.0.1",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",
@@ -78,7 +78,7 @@
     "ts-jest": "^29.0.3",
     "typescript": "^5.0.3",
     "url": "^0.11.0",
-    "webpack": "5.89.0",
+    "webpack": "^5.89.0",
     "webpack-cli": "^5.0.1"
   },
   "publishConfig": {

package/src/sam.ts CHANGED Viewed

@@ -1,20 +1,36 @@
-export type HeaderDataItem = {
-  tag: string
-  data: Array<{ tag: string; value: string }>
-}
-export function parseHeaderText(text: string): HeaderDataItem[] {
+export function parseHeaderText(text: string) {
   const lines = text.split(/\r?\n/)
-  const data: HeaderDataItem[] = []
-  lines.forEach(line => {
+  const data: {
+    tag: string
+    data: {
+      tag: string
+      value: string | undefined
+    }[]
+  }[] = []
+  for (const line of lines) {
     const [tag, ...fields] = line.split(/\t/)
-    const parsedFields = fields.map(f => {
-      const [fieldTag, value] = f.split(':', 2)
-      return { tag: fieldTag, value }
-    })
     if (tag) {
-      data.push({ tag: tag.substr(1), data: parsedFields })
+      data.push({
+        tag: tag.slice(1),
+        data: fields.map(f => {
+          const r = f.indexOf(':')
+          if (r !== -1) {
+            return {
+              tag: f.slice(0, r),
+              value: f.slice(r + 1),
+            }
+          } else {
+            // @CO lines are not comma separated.
+            // See "samtools view -H c2\#pad.3.0.cram"
+            // so, just store value tag itself
+            return {
+              tag: f,
+              value: undefined,
+            }
+          }
+        }),
+      })
     }
-  })
+  }
   return data
 }