@gmod/bam 7.0.5 → 7.0.6

package/CHANGELOG.md

@@ -1,3 +1,7 @@
+## [7.0.6](https://github.com/GMOD/bam-js/compare/v7.0.5...v7.0.6) (2025-11-28)
+
+
+
 ## [7.0.5](https://github.com/GMOD/bam-js/compare/v7.0.4...v7.0.5) (2025-11-27)
 
 

package/dist/bamFile.d.ts

@@ -70,7 +70,7 @@ export default class BamFile {
         dpositions: number[];
         chunk: Chunk;
     }>;
-    readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk, chrId?: number, min?: number, max?: number): Promise<BAMFeature[]>;
+    readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<BAMFeature[]>;
     _shouldIncludeFeature(dataView: DataView, blockStart: number, chrId: number, max: number): boolean;
     hasRefSeq(seqName: string): Promise<boolean | undefined>;
     lineCount(seqName: string): Promise<number>;

package/dist/bamFile.js

@@ -153,7 +153,7 @@ class BamFile {
                 chunk,
                 opts,
             });
-            const records = await this.readBamFeatures(data, cpositions, dpositions, chunk, chrId, min, max);
+            const records = await this.readBamFeatures(data, cpositions, dpositions, chunk);
             const recs = [];
             for (const feature of records) {
                 if (feature.ref_id === chrId) {
@@ -243,14 +243,13 @@ class BamFile {
         const { buffer: data, cpositions, dpositions, } = await (0, bgzf_filehandle_1.unzipChunkSlice)(buf, chunk, this.cache);
         return { data, cpositions, dpositions, chunk };
     }
-    async readBamFeatures(ba, cpositions, dpositions, chunk, chrId, min, max) {
+    async readBamFeatures(ba, cpositions, dpositions, chunk) {
         let blockStart = 0;
         const sink = [];
         let pos = 0;
         const dataView = new DataView(ba.buffer);
         const hasDpositions = dpositions.length > 0;
         const hasCpositions = cpositions.length > 0;
-        const hasFilter = chrId !== undefined && min !== undefined && max !== undefined;
         while (blockStart + 4 < ba.length) {
             const blockSize = dataView.getInt32(blockStart, true);
             const blockEnd = blockStart + 4 + blockSize - 1;
@@ -259,12 +258,6 @@ class BamFile {
                 pos--;
             }
             if (blockEnd < ba.length) {
-                if (hasFilter &&
-                    blockStart + 12 < ba.length &&
-                    !this._shouldIncludeFeature(dataView, blockStart, chrId, max)) {
-                    blockStart = blockEnd + 1;
-                    continue;
-                }
                 const feature = new record_ts_1.default({
                     bytes: {
                         byteArray: ba,

package/dist/bamFile.js.map

@@ -1 +1 @@
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package/esm/bamFile.d.ts

@@ -70,7 +70,7 @@ export default class BamFile {
         dpositions: number[];
         chunk: Chunk;
     }>;
-    readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk, chrId?: number, min?: number, max?: number): Promise<BAMFeature[]>;
+    readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<BAMFeature[]>;
     _shouldIncludeFeature(dataView: DataView, blockStart: number, chrId: number, max: number): boolean;
     hasRefSeq(seqName: string): Promise<boolean | undefined>;
     lineCount(seqName: string): Promise<number>;

package/esm/bamFile.js

@@ -147,7 +147,7 @@ export default class BamFile {
                 chunk,
                 opts,
             });
-            const records = await this.readBamFeatures(data, cpositions, dpositions, chunk, chrId, min, max);
+            const records = await this.readBamFeatures(data, cpositions, dpositions, chunk);
             const recs = [];
             for (const feature of records) {
                 if (feature.ref_id === chrId) {
@@ -237,14 +237,13 @@ export default class BamFile {
         const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buf, chunk, this.cache);
         return { data, cpositions, dpositions, chunk };
     }
-    async readBamFeatures(ba, cpositions, dpositions, chunk, chrId, min, max) {
+    async readBamFeatures(ba, cpositions, dpositions, chunk) {
         let blockStart = 0;
         const sink = [];
         let pos = 0;
         const dataView = new DataView(ba.buffer);
         const hasDpositions = dpositions.length > 0;
         const hasCpositions = cpositions.length > 0;
-        const hasFilter = chrId !== undefined && min !== undefined && max !== undefined;
         while (blockStart + 4 < ba.length) {
             const blockSize = dataView.getInt32(blockStart, true);
             const blockEnd = blockStart + 4 + blockSize - 1;
@@ -253,12 +252,6 @@ export default class BamFile {
                 pos--;
             }
             if (blockEnd < ba.length) {
-                if (hasFilter &&
-                    blockStart + 12 < ba.length &&
-                    !this._shouldIncludeFeature(dataView, blockStart, chrId, max)) {
-                    blockStart = blockEnd + 1;
-                    continue;
-                }
                 const feature = new BAMFeature({
                     bytes: {
                         byteArray: ba,

package/esm/bamFile.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "7.0.5",
+  "version": "7.0.6",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": "GMOD/bam-js",

package/src/bamFile.ts

@@ -227,9 +227,6 @@ export default class BamFile {
         cpositions,
         dpositions,
         chunk,
-        chrId,
-        min,
-        max,
       )
 
       const recs = [] as BAMFeature[]
@@ -352,9 +349,6 @@ export default class BamFile {
     cpositions: number[],
     dpositions: number[],
     chunk: Chunk,
-    chrId?: number,
-    min?: number,
-    max?: number,
   ) {
     let blockStart = 0
     const sink = [] as BAMFeature[]
@@ -363,8 +357,6 @@ export default class BamFile {
     const dataView = new DataView(ba.buffer)
     const hasDpositions = dpositions.length > 0
     const hasCpositions = cpositions.length > 0
-    const hasFilter =
-      chrId !== undefined && min !== undefined && max !== undefined
 
     while (blockStart + 4 < ba.length) {
       const blockSize = dataView.getInt32(blockStart, true)
@@ -376,15 +368,6 @@ export default class BamFile {
       }
 
       if (blockEnd < ba.length) {
-        if (
-          hasFilter &&
-          blockStart + 12 < ba.length &&
-          !this._shouldIncludeFeature(dataView, blockStart, chrId, max)
-        ) {
-          blockStart = blockEnd + 1
-          continue
-        }
-
         const feature = new BAMFeature({
           bytes: {
             byteArray: ba,