@gmod/bam - npm Package Compare versions

Comparing version 1.1.11 to 1.1.12

CHANGELOG.md

@@ -0,1 +1,8 @@
+<a name="1.1.12"></a>
+## [1.1.12](https://github.com/GMOD/bam-js/compare/v1.1.11...v1.1.12) (2022-02-17)
+
+
+
+- Add blocksForRange method to BamFile class to help stats estimation in JBrowse 2
+
 <a name="1.1.11"></a>
@@ -2,0 +9,0 @@ ## [1.1.11](https://github.com/GMOD/bam-js/compare/v1.1.10...v1.1.11) (2022-01-26)

dist/bai.js

@@ -282,4 +282,3 @@ "use strict";
                         }
-                        overlappingBins = this.reg2bins(min, max) // List of bin #s that overlap min, max
-                        ;
+                        overlappingBins = this.reg2bins(min, max);
                         chunks = [];
@@ -286,0 +285,0 @@ // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned

dist/bamFile.d.ts

@@ -77,2 +77,3 @@ /// <reference types="node" />
     }[]>;
+    blocksForRange(seqName: string, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
 }

dist/bamFile.js

@@ -687,2 +687,16 @@ "use strict";
     };
+    BamFile.prototype.blocksForRange = function (seqName, start, end, opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var seqId;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.index.parse()];
+                    case 1:
+                        _a.sent();
+                        seqId = this.chrToIndex && this.chrToIndex[seqName];
+                        return [2 /*return*/, this.index.blocksForRange(seqId, start, end, opts)];
+                }
+            });
+        });
+    };
     return BamFile;
@@ -689,0 +703,0 @@ }());

dist/indexFile.d.ts

@@ -24,3 +24,3 @@ import { GenericFilehandle } from 'generic-filehandle';
     }[]>;
-    abstract blocksForRange(chrId: number, start: number, end: number, opts: BaseOpts): Promise<Chunk[]>;
+    abstract blocksForRange(chrId: number, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
     _findFirstData(data: any, virtualOffset: VirtualOffset): void;
@@ -27,0 +27,0 @@ parse(opts?: BaseOpts): Promise<any>;

esm/bai.js

@@ -162,3 +162,4 @@ import Long from 'long';
         }
-        const overlappingBins = this.reg2bins(min, max); // List of bin #s that overlap min, max
+        // List of bin #s that overlap min, max
+        const overlappingBins = this.reg2bins(min, max);
         const chunks = [];
@@ -176,3 +177,4 @@ // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
         }
-        // Use the linear index to find minimum file position of chunks that could contain alignments in the region
+        // Use the linear index to find minimum file position of chunks that could
+        // contain alignments in the region
         const nintv = ba.linearIndex.length;
@@ -179,0 +181,0 @@ let lowest = null;

esm/bamFile.d.ts

@@ -77,2 +77,3 @@ /// <reference types="node" />
     }[]>;
+    blocksForRange(seqName: string, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
 }

esm/bamFile.js

@@ -382,3 +382,8 @@ import BAI from './bai';
     }
+    async blocksForRange(seqName, start, end, opts) {
+        await this.index.parse();
+        const seqId = this.chrToIndex && this.chrToIndex[seqName];
+        return this.index.blocksForRange(seqId, start, end, opts);
+    }
 }
 //# sourceMappingURL=bamFile.js.map

esm/indexFile.d.ts

@@ -24,3 +24,3 @@ import { GenericFilehandle } from 'generic-filehandle';
     }[]>;
-    abstract blocksForRange(chrId: number, start: number, end: number, opts: BaseOpts): Promise<Chunk[]>;
+    abstract blocksForRange(chrId: number, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
     _findFirstData(data: any, virtualOffset: VirtualOffset): void;
@@ -27,0 +27,0 @@ parse(opts?: BaseOpts): Promise<any>;

package.json

 {
   "name": "@gmod/bam",
-  "version": "1.1.11",
+  "version": "1.1.12",
   "description": "Parser for BAM and BAM index (bai) files",
@@ -5,0 +5,0 @@ "license": "MIT",

New alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

353975

increased by0.5%

Lines of code

5125

increased by0.43%

No dependency changes