npm - @gmod/bam - Versions diffs - 7.1.1 → 7.1.2 - Mend

@gmod/bam 7.1.1 → 7.1.2

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 (31) hide show

package/CHANGELOG.md CHANGED Viewed

@@ -1,3 +1,7 @@
+## [7.1.2](https://github.com/GMOD/bam-js/compare/v7.1.1...v7.1.2) (2025-12-12)
 ## [7.1.1](https://github.com/GMOD/bam-js/compare/v7.1.0...v7.1.1) (2025-12-12)

package/dist/bai.js CHANGED Viewed

@@ -206,28 +206,24 @@ class BAI extends indexFile_ts_1.default {
         const overlappingBins = reg2bins(min, max);
         const chunks = [];
         // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
+        const { binIndex } = ba;
         for (const [start, end] of overlappingBins) {
             for (let bin = start; bin <= end; bin++) {
-                if (ba.binIndex[bin]) {
-                    const binChunks = ba.binIndex[bin];
-                    for (const binChunk of binChunks) {
-                        chunks.push(new chunk_ts_1.default(binChunk.minv, binChunk.maxv, bin));
+                const binChunks = binIndex[bin];
+                if (binChunks) {
+                    for (let i = 0, l = binChunks.length; i < l; i++) {
+                        chunks.push(binChunks[i]);
                     }
                 }
             }
         }
         // Use the linear index to find minimum file position of chunks that could
-        // contain alignments in the region
-        const nintv = ba.linearIndex.length;
-        let lowest;
+        // contain alignments in the region. Linear index entries are monotonically
+        // non-decreasing, so the first entry at minLin is the minimum.
+        const { linearIndex } = ba;
+        const nintv = linearIndex.length;
         const minLin = Math.min(min >> 14, nintv - 1);
-        const maxLin = Math.min(max >> 14, nintv - 1);
-        for (let i = minLin; i <= maxLin; ++i) {
-            const vp = ba.linearIndex[i];
-            if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
-                lowest = vp;
-            }
-        }
+        const lowest = linearIndex[minLin];
         return (0, util_ts_1.optimizeChunks)(chunks, lowest);
     }
     async parse(opts = {}) {

package/dist/bai.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/bamFile.d.ts CHANGED Viewed

@@ -86,4 +86,9 @@ export default class BamFile {
     indexCov(seqName: string, start?: number, end?: number): Promise<import("./bai.ts").IndexCovEntry[]>;
     blocksForRange(seqName: string, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
     clearFeatureCache(): void;
+    estimatedBytesForRegions(regions: {
+        refName: string;
+        start: number;
+        end: number;
+    }[], opts?: BaseOpts): Promise<number>;
 }

package/dist/bamFile.js CHANGED Viewed

@@ -357,6 +357,23 @@ class BamFile {
     clearFeatureCache() {
         this.chunkFeatureCache.clear();
     }
+    async estimatedBytesForRegions(regions, opts) {
+        if (!this.index) {
+            return 0;
+        }
+        await this.getHeader(opts);
+        if (!this.chrToIndex) {
+            throw new Error('Header not yet parsed');
+        }
+        const regionsWithIds = regions.map(r => {
+            const refId = this.chrToIndex[r.refName];
+            if (refId === undefined) {
+                throw new Error(`Unknown reference name: ${r.refName}`);
+            }
+            return { refId, start: r.start, end: r.end };
+        });
+        return this.index.estimatedBytesForRegions(regionsWithIds, opts);
+    }
 }
 exports.default = BamFile;
 //# sourceMappingURL=bamFile.js.map

package/dist/bamFile.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/csi.js CHANGED Viewed

@@ -185,12 +185,13 @@ class CSI extends indexFile_ts_1.default {
         }
         const chunks = [];
         // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
+        const { binIndex } = ba;
         for (const [start, end] of overlappingBins) {
             for (let bin = start; bin <= end; bin++) {
-                if (ba.binIndex[bin]) {
-                    const binChunks = ba.binIndex[bin];
-                    for (const c of binChunks) {
-                        chunks.push(c);
+                const binChunks = binIndex[bin];
+                if (binChunks) {
+                    for (let i = 0, l = binChunks.length; i < l; i++) {
+                        chunks.push(binChunks[i]);
                     }
                 }
             }

package/dist/csi.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/indexFile.d.ts CHANGED Viewed

@@ -1,6 +1,11 @@
 import Chunk from './chunk.ts';
 import { BaseOpts } from './util.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
+export interface Region {
+    refId: number;
+    start: number;
+    end: number;
+}
 export default abstract class IndexFile {
     filehandle: GenericFilehandle;
     renameRefSeq: (s: string) => string;
@@ -15,4 +20,5 @@ export default abstract class IndexFile {
         score: number;
     }[]>;
     abstract blocksForRange(chrId: number, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
+    estimatedBytesForRegions(regions: Region[], opts?: BaseOpts): Promise<number>;
 }

package/dist/indexFile.js CHANGED Viewed

@@ -1,10 +1,21 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+const util_ts_1 = require("./util.js");
 class IndexFile {
     constructor({ filehandle, renameRefSeq = (n) => n, }) {
         this.filehandle = filehandle;
         this.renameRefSeq = renameRefSeq;
     }
+    async estimatedBytesForRegions(regions, opts) {
+        const blockResults = await Promise.all(regions.map(r => this.blocksForRange(r.refId, r.start, r.end, opts)));
+        // Deduplicate and merge overlapping blocks across all regions
+        const mergedBlocks = (0, util_ts_1.optimizeChunks)(blockResults.flat());
+        let total = 0;
+        for (const block of mergedBlocks) {
+            total += block.fetchedSize();
+        }
+        return total;
+    }
 }
 exports.default = IndexFile;
 //# sourceMappingURL=indexFile.js.map

package/dist/indexFile.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;~~AAKA~~,MAA8B,SAAS;IAIrC,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;~~CAcF~~;~~AA3BD~~,~~4BA2BC~~"}
1	+ {"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;AACA,uCAAoD;AAUpD,MAA8B,SAAS;IAIrC,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;IAeD,KAAK,CAAC,wBAAwB,CAAC,OAAiB,EAAE,IAAe;QAC/D,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC,CACrE,CAAA;QAED,8DAA8D;QAC9D,MAAM,YAAY,GAAG,IAAA,wBAAc,EAAC,YAAY,CAAC,IAAI,EAAE,CAAC,CAAA;QAExD,IAAI,KAAK,GAAG,CAAC,CAAA;QACb,KAAK,MAAM,KAAK,IAAI,YAAY,EAAE,CAAC;YACjC,KAAK,IAAI,KAAK,CAAC,WAAW,EAAE,CAAA;QAC9B,CAAC;QACD,OAAO,KAAK,CAAA;IACd,CAAC;CACF;AA1CD,4BA0CC"}

package/dist/util.js CHANGED Viewed

@@ -17,33 +17,62 @@ function makeOpts(obj = {}) {
     return 'aborted' in obj ? { signal: obj } : obj;
 }
 function optimizeChunks(chunks, lowest) {
-    const mergedChunks = [];
-    let lastChunk;
-    if (chunks.length === 0) {
+    const n = chunks.length;
+    if (n === 0) {
         return chunks;
     }
-    chunks.sort((c0, c1) => {
+    // Pre-filter chunks below lowest threshold before sorting
+    let filtered;
+    if (lowest) {
+        const lowestBlock = lowest.blockPosition;
+        const lowestData = lowest.dataPosition;
+        filtered = [];
+        for (let i = 0; i < n; i++) {
+            const chunk = chunks[i];
+            const maxv = chunk.maxv;
+            const cmp = maxv.blockPosition - lowestBlock || maxv.dataPosition - lowestData;
+            if (cmp > 0) {
+                filtered.push(chunk);
+            }
+        }
+        if (filtered.length === 0) {
+            return filtered;
+        }
+    }
+    else {
+        filtered = chunks;
+    }
+    filtered.sort((c0, c1) => {
         const dif = c0.minv.blockPosition - c1.minv.blockPosition;
-        return dif === 0 ? c0.minv.dataPosition - c1.minv.dataPosition : dif;
+        return dif !== 0 ? dif : c0.minv.dataPosition - c1.minv.dataPosition;
     });
-    for (const chunk of chunks) {
-        if (!lowest || chunk.maxv.compareTo(lowest) > 0) {
-            if (lastChunk === undefined) {
-                mergedChunks.push(chunk);
-                lastChunk = chunk;
-            }
-            else {
-                if (canMergeBlocks(lastChunk, chunk)) {
-                    if (chunk.maxv.compareTo(lastChunk.maxv) > 0) {
-                        lastChunk.maxv = chunk.maxv;
-                    }
-                }
-                else {
-                    mergedChunks.push(chunk);
-                    lastChunk = chunk;
-                }
+    const mergedChunks = [];
+    let lastChunk = filtered[0];
+    mergedChunks.push(lastChunk);
+    let lastMinBlock = lastChunk.minv.blockPosition;
+    let lastMaxBlock = lastChunk.maxv.blockPosition;
+    for (let i = 1; i < filtered.length; i++) {
+        const chunk = filtered[i];
+        const chunkMinBlock = chunk.minv.blockPosition;
+        const chunkMaxBlock = chunk.maxv.blockPosition;
+        // Inlined canMergeBlocks: check if chunks are close enough to merge
+        if (chunkMinBlock - lastMaxBlock < 65000 &&
+            chunkMaxBlock - lastMinBlock < 5000000) {
+            const chunkMaxv = chunk.maxv;
+            const lastMaxv = lastChunk.maxv;
+            const cmp = chunkMaxBlock - lastMaxBlock ||
+                chunkMaxv.dataPosition - lastMaxv.dataPosition;
+            if (cmp > 0) {
+                lastChunk.maxv = chunkMaxv;
+                lastMaxBlock = chunkMaxBlock;
             }
         }
+        else {
+            mergedChunks.push(chunk);
+            lastChunk = chunk;
+            lastMinBlock = chunkMinBlock;
+            lastMaxBlock = chunkMaxBlock;
+        }
     }
     return mergedChunks;
 }

package/dist/util.js.map CHANGED Viewed

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

@@ -201,28 +201,24 @@ export default class BAI extends IndexFile {
         const overlappingBins = reg2bins(min, max);
         const chunks = [];
         // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
+        const { binIndex } = ba;
         for (const [start, end] of overlappingBins) {
             for (let bin = start; bin <= end; bin++) {
-                if (ba.binIndex[bin]) {
-                    const binChunks = ba.binIndex[bin];
-                    for (const binChunk of binChunks) {
-                        chunks.push(new Chunk(binChunk.minv, binChunk.maxv, bin));
+                const binChunks = binIndex[bin];
+                if (binChunks) {
+                    for (let i = 0, l = binChunks.length; i < l; i++) {
+                        chunks.push(binChunks[i]);
                     }
                 }
             }
         }
         // Use the linear index to find minimum file position of chunks that could
-        // contain alignments in the region
-        const nintv = ba.linearIndex.length;
-        let lowest;
+        // contain alignments in the region. Linear index entries are monotonically
+        // non-decreasing, so the first entry at minLin is the minimum.
+        const { linearIndex } = ba;
+        const nintv = linearIndex.length;
         const minLin = Math.min(min >> 14, nintv - 1);
-        const maxLin = Math.min(max >> 14, nintv - 1);
-        for (let i = minLin; i <= maxLin; ++i) {
-            const vp = ba.linearIndex[i];
-            if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
-                lowest = vp;
-            }
-        }
+        const lowest = linearIndex[minLin];
         return optimizeChunks(chunks, lowest);
     }
     async parse(opts = {}) {

package/esm/bai.js.map CHANGED Viewed

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

@@ -86,4 +86,9 @@ export default class BamFile {
     indexCov(seqName: string, start?: number, end?: number): Promise<import("./bai.ts").IndexCovEntry[]>;
     blocksForRange(seqName: string, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
     clearFeatureCache(): void;
+    estimatedBytesForRegions(regions: {
+        refName: string;
+        start: number;
+        end: number;
+    }[], opts?: BaseOpts): Promise<number>;
 }

package/esm/bamFile.js CHANGED Viewed

@@ -351,5 +351,22 @@ export default class BamFile {
     clearFeatureCache() {
         this.chunkFeatureCache.clear();
     }
+    async estimatedBytesForRegions(regions, opts) {
+        if (!this.index) {
+            return 0;
+        }
+        await this.getHeader(opts);
+        if (!this.chrToIndex) {
+            throw new Error('Header not yet parsed');
+        }
+        const regionsWithIds = regions.map(r => {
+            const refId = this.chrToIndex[r.refName];
+            if (refId === undefined) {
+                throw new Error(`Unknown reference name: ${r.refName}`);
+            }
+            return { refId, start: r.start, end: r.end };
+        });
+        return this.index.estimatedBytesForRegions(regionsWithIds, opts);
+    }
 }
 //# sourceMappingURL=bamFile.js.map

package/esm/bamFile.js.map CHANGED Viewed

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

@@ -180,12 +180,13 @@ export default class CSI extends IndexFile {
         }
         const chunks = [];
         // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
+        const { binIndex } = ba;
         for (const [start, end] of overlappingBins) {
             for (let bin = start; bin <= end; bin++) {
-                if (ba.binIndex[bin]) {
-                    const binChunks = ba.binIndex[bin];
-                    for (const c of binChunks) {
-                        chunks.push(c);
+                const binChunks = binIndex[bin];
+                if (binChunks) {
+                    for (let i = 0, l = binChunks.length; i < l; i++) {
+                        chunks.push(binChunks[i]);
                     }
                 }
             }

package/esm/csi.js.map CHANGED Viewed

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

@@ -1,6 +1,11 @@
 import Chunk from './chunk.ts';
 import { BaseOpts } from './util.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
+export interface Region {
+    refId: number;
+    start: number;
+    end: number;
+}
 export default abstract class IndexFile {
     filehandle: GenericFilehandle;
     renameRefSeq: (s: string) => string;
@@ -15,4 +20,5 @@ export default abstract class IndexFile {
         score: number;
     }[]>;
     abstract blocksForRange(chrId: number, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
+    estimatedBytesForRegions(regions: Region[], opts?: BaseOpts): Promise<number>;
 }

package/esm/indexFile.js CHANGED Viewed

@@ -1,7 +1,18 @@
+import { optimizeChunks } from "./util.js";
 export default class IndexFile {
     constructor({ filehandle, renameRefSeq = (n) => n, }) {
         this.filehandle = filehandle;
         this.renameRefSeq = renameRefSeq;
     }
+    async estimatedBytesForRegions(regions, opts) {
+        const blockResults = await Promise.all(regions.map(r => this.blocksForRange(r.refId, r.start, r.end, opts)));
+        // Deduplicate and merge overlapping blocks across all regions
+        const mergedBlocks = optimizeChunks(blockResults.flat());
+        let total = 0;
+        for (const block of mergedBlocks) {
+            total += block.fetchedSize();
+        }
+        return total;
+    }
 }
 //# sourceMappingURL=indexFile.js.map

package/esm/indexFile.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"~~AAKA~~,MAAM,CAAC,OAAO,OAAgB,SAAS;IAIrC,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;~~CAcF~~"}
1	+ {"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AACA,OAAO,EAAY,cAAc,EAAE,MAAM,WAAW,CAAA;AAUpD,MAAM,CAAC,OAAO,OAAgB,SAAS;IAIrC,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;IAeD,KAAK,CAAC,wBAAwB,CAAC,OAAiB,EAAE,IAAe;QAC/D,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC,CACrE,CAAA;QAED,8DAA8D;QAC9D,MAAM,YAAY,GAAG,cAAc,CAAC,YAAY,CAAC,IAAI,EAAE,CAAC,CAAA;QAExD,IAAI,KAAK,GAAG,CAAC,CAAA;QACb,KAAK,MAAM,KAAK,IAAI,YAAY,EAAE,CAAC;YACjC,KAAK,IAAI,KAAK,CAAC,WAAW,EAAE,CAAA;QAC9B,CAAC;QACD,OAAO,KAAK,CAAA;IACd,CAAC;CACF"}

package/esm/util.js CHANGED Viewed

@@ -7,33 +7,62 @@ export function makeOpts(obj = {}) {
     return 'aborted' in obj ? { signal: obj } : obj;
 }
 export function optimizeChunks(chunks, lowest) {
-    const mergedChunks = [];
-    let lastChunk;
-    if (chunks.length === 0) {
+    const n = chunks.length;
+    if (n === 0) {
         return chunks;
     }
-    chunks.sort((c0, c1) => {
+    // Pre-filter chunks below lowest threshold before sorting
+    let filtered;
+    if (lowest) {
+        const lowestBlock = lowest.blockPosition;
+        const lowestData = lowest.dataPosition;
+        filtered = [];
+        for (let i = 0; i < n; i++) {
+            const chunk = chunks[i];
+            const maxv = chunk.maxv;
+            const cmp = maxv.blockPosition - lowestBlock || maxv.dataPosition - lowestData;
+            if (cmp > 0) {
+                filtered.push(chunk);
+            }
+        }
+        if (filtered.length === 0) {
+            return filtered;
+        }
+    }
+    else {
+        filtered = chunks;
+    }
+    filtered.sort((c0, c1) => {
         const dif = c0.minv.blockPosition - c1.minv.blockPosition;
-        return dif === 0 ? c0.minv.dataPosition - c1.minv.dataPosition : dif;
+        return dif !== 0 ? dif : c0.minv.dataPosition - c1.minv.dataPosition;
     });
-    for (const chunk of chunks) {
-        if (!lowest || chunk.maxv.compareTo(lowest) > 0) {
-            if (lastChunk === undefined) {
-                mergedChunks.push(chunk);
-                lastChunk = chunk;
-            }
-            else {
-                if (canMergeBlocks(lastChunk, chunk)) {
-                    if (chunk.maxv.compareTo(lastChunk.maxv) > 0) {
-                        lastChunk.maxv = chunk.maxv;
-                    }
-                }
-                else {
-                    mergedChunks.push(chunk);
-                    lastChunk = chunk;
-                }
+    const mergedChunks = [];
+    let lastChunk = filtered[0];
+    mergedChunks.push(lastChunk);
+    let lastMinBlock = lastChunk.minv.blockPosition;
+    let lastMaxBlock = lastChunk.maxv.blockPosition;
+    for (let i = 1; i < filtered.length; i++) {
+        const chunk = filtered[i];
+        const chunkMinBlock = chunk.minv.blockPosition;
+        const chunkMaxBlock = chunk.maxv.blockPosition;
+        // Inlined canMergeBlocks: check if chunks are close enough to merge
+        if (chunkMinBlock - lastMaxBlock < 65000 &&
+            chunkMaxBlock - lastMinBlock < 5000000) {
+            const chunkMaxv = chunk.maxv;
+            const lastMaxv = lastChunk.maxv;
+            const cmp = chunkMaxBlock - lastMaxBlock ||
+                chunkMaxv.dataPosition - lastMaxv.dataPosition;
+            if (cmp > 0) {
+                lastChunk.maxv = chunkMaxv;
+                lastMaxBlock = chunkMaxBlock;
             }
         }
+        else {
+            mergedChunks.push(chunk);
+            lastChunk = chunk;
+            lastMinBlock = chunkMinBlock;
+            lastMaxBlock = chunkMaxBlock;
+        }
     }
     return mergedChunks;
 }

package/esm/util.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,uBAAuB,EAAE,MAAM,WAAW,CAAA;AAGnD,MAAM,UAAU,cAAc,CAAC,MAAa,EAAE,MAAa;IACzD,OAAO,CACL,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,KAAK;QAC7D,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,OAAO,CAChE,CAAA;AACH,CAAC;AAaD,MAAM,UAAU,QAAQ,CAAC,MAA8B,EAAE;IACvD,OAAO,SAAS,IAAI,GAAG,CAAC,CAAC,CAAE,EAAE,MAAM,EAAE,GAAG,EAAe,CAAC,CAAC,CAAC,GAAG,CAAA;AAC/D,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,MAAe,EAAE,MAAe;IAC7D,MAAM,CAAC,GAAG,MAAM,CAAC,MAAM,CAAA;IACvB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QACZ,OAAO,MAAM,CAAA;IACf,CAAC;IAED,0DAA0D;IAC1D,IAAI,QAAiB,CAAA;IACrB,IAAI,MAAM,EAAE,CAAC;QACX,MAAM,WAAW,GAAG,MAAM,CAAC,aAAa,CAAA;QACxC,MAAM,UAAU,GAAG,MAAM,CAAC,YAAY,CAAA;QACtC,QAAQ,GAAG,EAAE,CAAA;QACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YAC3B,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;YACxB,MAAM,IAAI,GAAG,KAAK,CAAC,IAAI,CAAA;YACvB,MAAM,GAAG,GACP,IAAI,CAAC,aAAa,GAAG,WAAW,IAAI,IAAI,CAAC,YAAY,GAAG,UAAU,CAAA;YACpE,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACtB,CAAC;QACH,CAAC;QACD,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC1B,OAAO,QAAQ,CAAA;QACjB,CAAC;IACH,CAAC;SAAM,CAAC;QACN,QAAQ,GAAG,MAAM,CAAA;IACnB,CAAC;IAED,QAAQ,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE;QACvB,MAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAA;IACtE,CAAC,CAAC,CAAA;IAEF,MAAM,YAAY,GAAY,EAAE,CAAA;IAChC,IAAI,SAAS,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAA;IAC5B,YAAY,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;IAE5B,IAAI,YAAY,GAAG,SAAS,CAAC,IAAI,CAAC,aAAa,CAAA;IAC/C,IAAI,YAAY,GAAG,SAAS,CAAC,IAAI,CAAC,aAAa,CAAA;IAE/C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACzC,MAAM,KAAK,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAA;QAC1B,MAAM,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,aAAa,CAAA;QAC9C,MAAM,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,aAAa,CAAA;QAC9C,oEAAoE;QACpE,IACE,aAAa,GAAG,YAAY,GAAG,KAAK;YACpC,aAAa,GAAG,YAAY,GAAG,OAAO,EACtC,CAAC;YACD,MAAM,SAAS,GAAG,KAAK,CAAC,IAAI,CAAA;YAC5B,MAAM,QAAQ,GAAG,SAAS,CAAC,IAAI,CAAA;YAC/B,MAAM,GAAG,GACP,aAAa,GAAG,YAAY;gBAC5B,SAAS,CAAC,YAAY,GAAG,QAAQ,CAAC,YAAY,CAAA;YAChD,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,SAAS,CAAC,IAAI,GAAG,SAAS,CAAA;gBAC1B,YAAY,GAAG,aAAa,CAAA;YAC9B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACxB,SAAS,GAAG,KAAK,CAAA;YACjB,YAAY,GAAG,aAAa,CAAA;YAC5B,YAAY,GAAG,aAAa,CAAA;QAC9B,CAAC;IACH,CAAC;IAED,OAAO,YAAY,CAAA;AACrB,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,KAAiB,EAAE,MAAc;IAC9D,OAAO;QACL,SAAS,EAAE,uBAAuB,CAAC,KAAK,EAAE,MAAM,CAAC;KAClD,CAAA;AACH,CAAC;AAED,MAAM,UAAU,aAAa,CAC3B,aAAwC,EACxC,aAA4B;IAE5B,OAAO,aAAa;QAClB,CAAC,CAAC,aAAa,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;YAC1C,CAAC,CAAC,aAAa;YACf,CAAC,CAAC,aAAa;QACjB,CAAC,CAAC,aAAa,CAAA;AACnB,CAAC;AAED,MAAM,UAAU,cAAc,CAC5B,UAAsB,EACtB,eAAwC,CAAC,CAAC,EAAE,CAAC,CAAC;IAE9C,IAAI,SAAS,GAAG,CAAC,CAAA;IACjB,IAAI,aAAa,GAAG,CAAC,CAAA;IACrB,MAAM,WAAW,GAAG,EAAE,CAAA;IACtB,MAAM,WAAW,GAA2B,EAAE,CAAA;IAC9C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QAC9C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;YACnB,IAAI,aAAa,GAAG,CAAC,EAAE,CAAC;gBACtB,IAAI,OAAO,GAAG,EAAE,CAAA;gBAChB,KAAK,IAAI,CAAC,GAAG,aAAa,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;oBACvC,OAAO,IAAI,MAAM,CAAC,YAAY,CAAC,UAAU,CAAC,CAAC,CAAE,CAAC,CAAA;gBAChD,CAAC;gBACD,OAAO,GAAG,YAAY,CAAC,OAAO,CAAC,CAAA;gBAC/B,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;gBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;YAClC,CAAC;YACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;YACrB,SAAS,IAAI,CAAC,CAAA;QAChB,CAAC;IACH,CAAC;IACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;AACrC,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,IAAkB;IACjD,IAAI,WAAW,GAAG,CAAC,CAAA;IACnB,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;QACzB,WAAW,IAAI,KAAK,CAAC,MAAM,CAAA;IAC7B,CAAC;IACD,MAAM,WAAW,GAAG,IAAI,UAAU,CAAC,WAAW,CAAC,CAAA;IAC/C,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;QACzB,WAAW,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAC9B,MAAM,IAAI,KAAK,CAAC,MAAM,CAAA;IACxB,CAAC;IACD,OAAO,WAAW,CAAA;AACpB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,SAAS,CAAI,GAAuB;IACxD,MAAM,GAAG,GAAQ,EAAE,CAAA;IACnB,IAAI,KAAK,EAAE,MAAM,CAAC,IAAI,GAAG,EAAE,CAAC;QAC1B,KAAK,MAAM,IAAI,IAAI,CAAC,EAAE,CAAC;YACrB,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAChB,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "7.1.1",
+  "version": "7.1.2",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": "GMOD/bam-js",
@@ -50,7 +50,7 @@
     "genomics"
   ],
   "dependencies": {
-    "@gmod/bgzf-filehandle": "^6.0.5",
+    "@gmod/bgzf-filehandle": "^6.0.6",
     "crc": "^4.3.2",
     "generic-filehandle2": "^2.0.16",
     "quick-lru": "^4.0.0"

package/src/bai.ts CHANGED Viewed

@@ -246,30 +246,25 @@ export default class BAI extends IndexFile {
     const chunks: Chunk[] = []
     // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
+    const { binIndex } = ba
     for (const [start, end] of overlappingBins) {
       for (let bin = start; bin <= end; bin++) {
-        if (ba.binIndex[bin]) {
-          const binChunks = ba.binIndex[bin]!
-          for (const binChunk of binChunks) {
-            chunks.push(new Chunk(binChunk.minv, binChunk.maxv, bin))
+        const binChunks = binIndex[bin]
+        if (binChunks) {
+          for (let i = 0, l = binChunks.length; i < l; i++) {
+            chunks.push(binChunks[i]!)
           }
         }
       }
     }
     // Use the linear index to find minimum file position of chunks that could
-    // contain alignments in the region
-    const nintv = ba.linearIndex.length
-    let lowest: VirtualOffset | undefined
+    // contain alignments in the region. Linear index entries are monotonically
+    // non-decreasing, so the first entry at minLin is the minimum.
+    const { linearIndex } = ba
+    const nintv = linearIndex.length
     const minLin = Math.min(min >> 14, nintv - 1)
-    const maxLin = Math.min(max >> 14, nintv - 1)
-    for (let i = minLin; i <= maxLin; ++i) {
-      const vp = ba.linearIndex[i]
-      if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
-        lowest = vp
-      }
-    }
+    const lowest = linearIndex[minLin]
     return optimizeChunks(chunks, lowest)
   }

package/src/bamFile.ts CHANGED Viewed

@@ -503,4 +503,25 @@ export default class BamFile {
   clearFeatureCache() {
     this.chunkFeatureCache.clear()
   }
+  async estimatedBytesForRegions(
+    regions: { refName: string; start: number; end: number }[],
+    opts?: BaseOpts,
+  ) {
+    if (!this.index) {
+      return 0
+    }
+    await this.getHeader(opts)
+    if (!this.chrToIndex) {
+      throw new Error('Header not yet parsed')
+    }
+    const regionsWithIds = regions.map(r => {
+      const refId = this.chrToIndex![r.refName]
+      if (refId === undefined) {
+        throw new Error(`Unknown reference name: ${r.refName}`)
+      }
+      return { refId, start: r.start, end: r.end }
+    })
+    return this.index.estimatedBytesForRegions(regionsWithIds, opts)
+  }
 }

package/src/csi.ts CHANGED Viewed

@@ -215,12 +215,13 @@ export default class CSI extends IndexFile {
     const chunks = []
     // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
+    const { binIndex } = ba
     for (const [start, end] of overlappingBins) {
       for (let bin = start; bin <= end; bin++) {
-        if (ba.binIndex[bin]) {
-          const binChunks = ba.binIndex[bin]!
-          for (const c of binChunks) {
-            chunks.push(c)
+        const binChunks = binIndex[bin]
+        if (binChunks) {
+          for (let i = 0, l = binChunks.length; i < l; i++) {
+            chunks.push(binChunks[i]!)
           }
         }
       }

package/src/indexFile.ts CHANGED Viewed

@@ -1,8 +1,14 @@
 import Chunk from './chunk.ts'
-import { BaseOpts } from './util.ts'
+import { BaseOpts, optimizeChunks } from './util.ts'
 import type { GenericFilehandle } from 'generic-filehandle2'
+export interface Region {
+  refId: number
+  start: number
+  end: number
+}
 export default abstract class IndexFile {
   public filehandle: GenericFilehandle
   public renameRefSeq: (s: string) => string
@@ -30,4 +36,19 @@ export default abstract class IndexFile {
     end: number,
     opts?: BaseOpts,
   ): Promise<Chunk[]>
+  async estimatedBytesForRegions(regions: Region[], opts?: BaseOpts) {
+    const blockResults = await Promise.all(
+      regions.map(r => this.blocksForRange(r.refId, r.start, r.end, opts)),
+    )
+    // Deduplicate and merge overlapping blocks across all regions
+    const mergedBlocks = optimizeChunks(blockResults.flat())
+    let total = 0
+    for (const block of mergedBlocks) {
+      total += block.fetchedSize()
+    }
+    return total
+  }
 }

package/src/util.ts CHANGED Viewed

@@ -25,33 +25,68 @@ export function makeOpts(obj: AbortSignal | BaseOpts = {}): BaseOpts {
 }
 export function optimizeChunks(chunks: Chunk[], lowest?: Offset) {
-  const mergedChunks: Chunk[] = []
-  let lastChunk: Chunk | undefined
-  if (chunks.length === 0) {
+  const n = chunks.length
+  if (n === 0) {
     return chunks
   }
-  chunks.sort((c0, c1) => {
+  // Pre-filter chunks below lowest threshold before sorting
+  let filtered: Chunk[]
+  if (lowest) {
+    const lowestBlock = lowest.blockPosition
+    const lowestData = lowest.dataPosition
+    filtered = []
+    for (let i = 0; i < n; i++) {
+      const chunk = chunks[i]!
+      const maxv = chunk.maxv
+      const cmp =
+        maxv.blockPosition - lowestBlock || maxv.dataPosition - lowestData
+      if (cmp > 0) {
+        filtered.push(chunk)
+      }
+    }
+    if (filtered.length === 0) {
+      return filtered
+    }
+  } else {
+    filtered = chunks
+  }
+  filtered.sort((c0, c1) => {
     const dif = c0.minv.blockPosition - c1.minv.blockPosition
-    return dif === 0 ? c0.minv.dataPosition - c1.minv.dataPosition : dif
+    return dif !== 0 ? dif : c0.minv.dataPosition - c1.minv.dataPosition
   })
-  for (const chunk of chunks) {
-    if (!lowest || chunk.maxv.compareTo(lowest) > 0) {
-      if (lastChunk === undefined) {
-        mergedChunks.push(chunk)
-        lastChunk = chunk
-      } else {
-        if (canMergeBlocks(lastChunk, chunk)) {
-          if (chunk.maxv.compareTo(lastChunk.maxv) > 0) {
-            lastChunk.maxv = chunk.maxv
-          }
-        } else {
-          mergedChunks.push(chunk)
-          lastChunk = chunk
-        }
+  const mergedChunks: Chunk[] = []
+  let lastChunk = filtered[0]!
+  mergedChunks.push(lastChunk)
+  let lastMinBlock = lastChunk.minv.blockPosition
+  let lastMaxBlock = lastChunk.maxv.blockPosition
+  for (let i = 1; i < filtered.length; i++) {
+    const chunk = filtered[i]!
+    const chunkMinBlock = chunk.minv.blockPosition
+    const chunkMaxBlock = chunk.maxv.blockPosition
+    // Inlined canMergeBlocks: check if chunks are close enough to merge
+    if (
+      chunkMinBlock - lastMaxBlock < 65000 &&
+      chunkMaxBlock - lastMinBlock < 5000000
+    ) {
+      const chunkMaxv = chunk.maxv
+      const lastMaxv = lastChunk.maxv
+      const cmp =
+        chunkMaxBlock - lastMaxBlock ||
+        chunkMaxv.dataPosition - lastMaxv.dataPosition
+      if (cmp > 0) {
+        lastChunk.maxv = chunkMaxv
+        lastMaxBlock = chunkMaxBlock
       }
+    } else {
+      mergedChunks.push(chunk)
+      lastChunk = chunk
+      lastMinBlock = chunkMinBlock
+      lastMaxBlock = chunkMaxBlock
     }
   }