npm - @gmod/cram - Versions diffs - 8.0.4 → 8.0.5 - Mend

@gmod/cram 8.0.4 → 8.0.5

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 (8) hide show

package/README.md +66 -71
package/dist/cram-bundle.js +1 -1
package/dist/cramFile/slice/index.js +16 -4
package/dist/cramFile/slice/index.js.map +1 -1
package/esm/cramFile/slice/index.js +16 -4
package/esm/cramFile/slice/index.js.map +1 -1
package/package.json +6 -5
package/src/cramFile/slice/index.ts +16 -4

package/dist/cramFile/slice/index.js CHANGED Viewed

@@ -62,13 +62,18 @@ function calculateMultiSegmentMatedTemplateLength(allRecords, _currentRecordNumb
     const matedRecords = getAllMatedRecords(thisRecord);
     const starts = matedRecords.map(r => r.alignmentStart);
     const ends = matedRecords.map(r => r.alignmentStart + r.readLength - 1);
-    const estimatedTemplateLength = Math.max(...ends) - Math.min(...starts) + 1;
+    const minStart = Math.min(...starts);
+    const estimatedTemplateLength = Math.max(...ends) - minStart + 1;
     if (estimatedTemplateLength >= 0) {
         matedRecords.forEach(r => {
             if (r.templateLength !== undefined) {
                 throw new errors_ts_1.CramMalformedError('mate pair group has some members that have template lengths already, this file seems malformed');
             }
-            r.templateLength = estimatedTemplateLength;
+            // sign per SAM spec: positive for leftmost, negative for rightmost
+            r.templateLength =
+                r.alignmentStart === minStart
+                    ? estimatedTemplateLength
+                    : -estimatedTemplateLength;
         });
     }
 }
@@ -83,8 +88,15 @@ function calculateIntraSliceMatePairTemplateLength(thisRecord, mateRecord) {
     const start = Math.min(thisRecord.alignmentStart, mateRecord.alignmentStart);
     const end = Math.max(thisRecord.alignmentStart + thisRecord.readLength - 1, mateRecord.alignmentStart + mateRecord.readLength - 1);
     const lengthEstimate = end - start + 1;
-    thisRecord.templateLength = lengthEstimate;
-    mateRecord.templateLength = lengthEstimate;
+    // sign per SAM spec: positive for leftmost, negative for rightmost
+    thisRecord.templateLength =
+        thisRecord.alignmentStart <= mateRecord.alignmentStart
+            ? lengthEstimate
+            : -lengthEstimate;
+    mateRecord.templateLength =
+        mateRecord.alignmentStart <= thisRecord.alignmentStart
+            ? lengthEstimate
+            : -lengthEstimate;
 }
 /**
  * establishes a mate-pair relationship between two records in the same slice.

package/dist/cramFile/slice/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/cramFile/slice/index.js CHANGED Viewed

@@ -24,13 +24,18 @@ function calculateMultiSegmentMatedTemplateLength(allRecords, _currentRecordNumb
     const matedRecords = getAllMatedRecords(thisRecord);
     const starts = matedRecords.map(r => r.alignmentStart);
     const ends = matedRecords.map(r => r.alignmentStart + r.readLength - 1);
-    const estimatedTemplateLength = Math.max(...ends) - Math.min(...starts) + 1;
+    const minStart = Math.min(...starts);
+    const estimatedTemplateLength = Math.max(...ends) - minStart + 1;
     if (estimatedTemplateLength >= 0) {
         matedRecords.forEach(r => {
             if (r.templateLength !== undefined) {
                 throw new CramMalformedError('mate pair group has some members that have template lengths already, this file seems malformed');
             }
-            r.templateLength = estimatedTemplateLength;
+            // sign per SAM spec: positive for leftmost, negative for rightmost
+            r.templateLength =
+                r.alignmentStart === minStart
+                    ? estimatedTemplateLength
+                    : -estimatedTemplateLength;
         });
     }
 }
@@ -45,8 +50,15 @@ function calculateIntraSliceMatePairTemplateLength(thisRecord, mateRecord) {
     const start = Math.min(thisRecord.alignmentStart, mateRecord.alignmentStart);
     const end = Math.max(thisRecord.alignmentStart + thisRecord.readLength - 1, mateRecord.alignmentStart + mateRecord.readLength - 1);
     const lengthEstimate = end - start + 1;
-    thisRecord.templateLength = lengthEstimate;
-    mateRecord.templateLength = lengthEstimate;
+    // sign per SAM spec: positive for leftmost, negative for rightmost
+    thisRecord.templateLength =
+        thisRecord.alignmentStart <= mateRecord.alignmentStart
+            ? lengthEstimate
+            : -lengthEstimate;
+    mateRecord.templateLength =
+        mateRecord.alignmentStart <= thisRecord.alignmentStart
+            ? lengthEstimate
+            : -lengthEstimate;
 }
 /**
  * establishes a mate-pair relationship between two records in the same slice.

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

	@@ -1 +1 @@
1	- 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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/cram",
-  "version": "8.0.4",
+  "version": "8.0.5",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",
@@ -58,21 +58,22 @@
     "md5": "^2.2.1"
   },
   "devDependencies": {
+    "@eslint/js": "^10.0.1",
     "@gmod/indexedfasta": "^5.0.2",
     "@types/md5": "^2.3.2",
     "@vitest/coverage-v8": "^4.0.18",
     "buffer": "^6.0.3",
     "documentation": "^14.0.3",
-    "eslint": "^9.29.0",
+    "eslint": "^10.0.2",
     "eslint-plugin-import": "^2.31.0",
     "eslint-plugin-unicorn": "^63.0.0",
     "mock-fs": "^5.2.0",
     "prettier": "^3.8.1",
-    "rimraf": "^6.0.1",
+    "rimraf": "^6.1.3",
     "typescript": "^5.7.0",
-    "typescript-eslint": "^8.54.0",
+    "typescript-eslint": "^8.56.1",
     "vitest": "^4.0.18",
-    "webpack": "^5.99.9",
+    "webpack": "^5.105.3",
     "webpack-cli": "^6.0.1"
   },
   "publishConfig": {

package/src/cramFile/slice/index.ts CHANGED Viewed

@@ -58,7 +58,8 @@ function calculateMultiSegmentMatedTemplateLength(
   const matedRecords = getAllMatedRecords(thisRecord)
   const starts = matedRecords.map(r => r.alignmentStart)
   const ends = matedRecords.map(r => r.alignmentStart + r.readLength - 1)
-  const estimatedTemplateLength = Math.max(...ends) - Math.min(...starts) + 1
+  const minStart = Math.min(...starts)
+  const estimatedTemplateLength = Math.max(...ends) - minStart + 1
   if (estimatedTemplateLength >= 0) {
     matedRecords.forEach(r => {
       if (r.templateLength !== undefined) {
@@ -66,7 +67,11 @@ function calculateMultiSegmentMatedTemplateLength(
           'mate pair group has some members that have template lengths already, this file seems malformed',
         )
       }
-      r.templateLength = estimatedTemplateLength
+      // sign per SAM spec: positive for leftmost, negative for rightmost
+      r.templateLength =
+        r.alignmentStart === minStart
+          ? estimatedTemplateLength
+          : -estimatedTemplateLength
     })
   }
 }
@@ -88,8 +93,15 @@ function calculateIntraSliceMatePairTemplateLength(
     mateRecord.alignmentStart + mateRecord.readLength - 1,
   )
   const lengthEstimate = end - start + 1
-  thisRecord.templateLength = lengthEstimate
-  mateRecord.templateLength = lengthEstimate
+  // sign per SAM spec: positive for leftmost, negative for rightmost
+  thisRecord.templateLength =
+    thisRecord.alignmentStart <= mateRecord.alignmentStart
+      ? lengthEstimate
+      : -lengthEstimate
+  mateRecord.templateLength =
+    mateRecord.alignmentStart <= thisRecord.alignmentStart
+      ? lengthEstimate
+      : -lengthEstimate
 }
 /**