npm - @gmod/bam - Versions diffs - 9.0.1 → 10.0.1 - Mend

@gmod/bam 9.0.1 → 10.0.1

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 (54) hide show

package/esm/indexFile.js CHANGED Viewed

@@ -1,6 +1,7 @@
 import { SharedReadCache } from '@gmod/shared-read-cache';
 import QuickLRU from '@jbrowse/quick-lru';
 import { chunksLikelyRead, optimizeChunks } from "./util.js";
+import { compareOffsets } from "./virtualOffset.js";
 // SYNC: ~/src/gmod/tabix-js/src/util.ts memoizeByRefId
 // LRU-cache the result of getIndices(refId) so repeated lookups for the same
 // reference don't re-walk the index bytes.
@@ -20,6 +21,52 @@ export function memoizeByRefId(getIndices, maxSize = 5) {
         return result;
     };
 }
+/**
+ * The virtual offset past which a coordinate-sorted file holds nothing
+ * overlapping `[.., end)`, from the binning index alone: htslib's `max_off`
+ * (`hts_itr_query` in hts.c).
+ *
+ * Walk right from the finest bin after the one holding `end - 1`, stepping up
+ * to the parent at every first child, so each bin visited begins at or past
+ * `end` and never overlaps the query. Every record in such a bin starts at or
+ * past `end`, so the first chunk of the first bin that exists is a record past
+ * the query, and in a sorted file so is every record after it.
+ *
+ * A bound, unlike the linear-index forecast in `chunksLikelyRead`: it rests on
+ * the same sort order `appendInRange` and the early stop already assume, and
+ * cannot drop a record they would keep. See ADR 0023 for why the caller drops
+ * whole merged chunks with it rather than trimming them.
+ */
+export function maxOffset(binIndex, end, minShift, depth) {
+    if (end > 2 ** (minShift + depth * 3)) {
+        return undefined;
+    }
+    const binCount = (8 ** (depth + 1) - 1) / 7;
+    let bin = (8 ** depth - 1) / 7 + Math.floor((end - 1) / 2 ** minShift) + 1;
+    if (bin >= binCount) {
+        bin = 0;
+    }
+    for (;;) {
+        while (bin % 8 === 1) {
+            bin = (bin - 1) / 8;
+        }
+        if (bin === 0) {
+            return undefined;
+        }
+        const chunks = binIndex[bin];
+        if (chunks?.length) {
+            let lowest = chunks[0].minv;
+            for (let i = 1; i < chunks.length; i++) {
+                const minv = chunks[i].minv;
+                if (compareOffsets(minv, lowest) < 0) {
+                    lowest = minv;
+                }
+            }
+            return lowest;
+        }
+        bin++;
+    }
+}
 export default class IndexFile {
     filehandle;
     renameRefSeq;
@@ -57,7 +104,16 @@ export default class IndexFile {
                 }
             }
         }
-        return optimizeChunks(chunks, this.getLowestChunk(ba, min));
+        const merged = optimizeChunks(chunks, this.getLowestChunk(ba, min));
+        const past = maxOffset(binIndex, max, this.minShift, this.depth);
+        if (past) {
+            let n = merged.length;
+            while (n > 0 && compareOffsets(merged[n - 1].minv, past) >= 0) {
+                n--;
+            }
+            merged.length = n;
+        }
+        return merged;
     }
     // SYNC: ~/src/gmod/tabix-js/src/indexFile.ts parse — same shape and the same
     // reasoning below.
@@ -115,7 +171,8 @@ export default class IndexFile {
      * exists — was being told 5.6x the truth on exactly the windows a reader
      * spends their time in, and cannot answer it by zooming: every window narrower
      * than a linear-index interval resolves to the same chunks and so to the same
-     * number.
+     * number. The table predates `max_off` (ADR 0023), which now drops most of
+     * the gap between the first two columns from `blocksForRange` itself.
      *
      * Still summed over merged chunks rather than per region, so two regions
      * sharing a chunk are charged for it once.

package/esm/indexFile.js.map CHANGED Viewed

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

@@ -63,6 +63,7 @@ export default class BamRecord {
     isDuplicate(): boolean;
     isSupplementary(): boolean;
     private _isCGTagPattern;
+    private _hasCGPlaceholder;
     private _computeLengthOnRef;
     private _computeNumericCigar;
     get length_on_ref(): number;

package/esm/record.js CHANGED Viewed

@@ -368,17 +368,18 @@ export default class BamRecord {
         return this.mq;
     }
     // QUAL is present whenever the record has bases — independent of the unmapped
-    // flag (unmapped reads routinely carry SEQ/QUAL). A zero-length SEQ means
-    // there is no quality to return.
+    // flag (unmapped reads routinely carry SEQ/QUAL). null for a zero-length SEQ,
+    // and for a QUAL of `*`, which BAM stores as 0xFF in every byte (SAMv1
+    // §4.2.3). htslib decides on the first byte alone, and so does this.
     get qual() {
         const seqLen = this.seq_length;
         if (seqLen === 0) {
             return null;
         }
-        else {
-            const p = this.seqStart + ((seqLen + 1) >> 1);
-            return this._byteArray.subarray(p, p + seqLen);
-        }
+        const p = this.seqStart + ((seqLen + 1) >> 1);
+        return this._byteArray[p] === 0xff
+            ? null
+            : this._byteArray.subarray(p, p + seqLen);
     }
     get strand() {
         return this.isReverseComplemented() ? -1 : 1;
@@ -399,7 +400,7 @@ export default class BamRecord {
         const seqLen = this.seq_length;
         return this.seqStart + ((seqLen + 1) >> 1) + seqLen;
     }
-    // batch fromCharCode: fastest for typical name lengths (see benchmarks/string-building.bench.ts)
+    // batch fromCharCode: fastest for typical name lengths (benchmarks/string-building.bench.ts, removed in 36a3968)
     //
     // Deliberately NOT memoized, unlike end/tags/length_on_ref. Consumers read a
     // read name about once — jbrowse-components' buildBaseFeatureData copies it
@@ -431,8 +432,8 @@ export default class BamRecord {
         return this._cachedTags;
     }
     getTag(tagName) {
-        if (this._cachedTags !== undefined) {
-            return this._cachedTags[tagName];
+        if (this._cachedTags !== undefined || tagName === 'CG') {
+            return this.tags[tagName];
         }
         return this._findTag(tagName, false);
     }
@@ -531,6 +532,9 @@ export default class BamRecord {
             tags[tag] = decodeTagValue(ba, this._dataView, type, valueStart, end, false);
             p = end;
         }
+        if (this._hasCGPlaceholder() && isNumericCigar(tags.CG)) {
+            delete tags.CG;
+        }
         return tags;
     }
     isPaired() {
@@ -569,7 +573,7 @@ export default class BamRecord {
     isSupplementary() {
         return !!(this.flags & Constants.BAM_FSUPPLEMENTARY);
     }
-    // Benchmark results for CIGAR parsing strategies (see benchmarks/cigar-lifecycle.bench.ts):
+    // Benchmark results for CIGAR parsing strategies (benchmarks/cigar-strategies.bench.ts, removed in 36a3968):
     //
     // Aligned data:
     //   - Plain array is 1.6-1.8x faster than Uint32Array for small CIGARs (≤50 ops)
@@ -592,12 +596,17 @@ export default class BamRecord {
         // htslib stores the placeholder as exactly two ops: <seqlen>S<reflen>N.
         if (numCigarOps === 2) {
             const cigop = this._dataView.getInt32(p, true);
-            return (cigop & 0xf) === CIGAR_SOFT_CLIP && cigop >> 4 === this.seq_length;
+            return ((cigop & 0xf) === CIGAR_SOFT_CLIP && cigop >>> 4 === this.seq_length);
         }
         else {
             return false;
         }
     }
+    // SAMv1 §4.2.2: with the placeholder and a CG tag, the tag is the CIGAR and
+    // a reader removes it from the tags, as htslib does
+    _hasCGPlaceholder() {
+        return this._isCGTagPattern(this.b0 + this.read_name_length, this.flag_nc & 0xffff);
+    }
     _computeLengthOnRef() {
         const flag_nc = this._dataView.getInt32(this._start + 16, true);
         if (flag_nc & (Constants.BAM_FUNMAP << 16)) {
@@ -610,7 +619,7 @@ export default class BamRecord {
             if ((cigop2 & 0xf) !== CIGAR_REF_SKIP) {
                 console.warn('CG tag with no N tag');
             }
-            return cigop2 >> 4;
+            return cigop2 >>> 4;
         }
         const absOffset = this._byteArray.byteOffset + p;
         if (absOffset % 4 === 0 && numCigarOps > 50) {
@@ -621,14 +630,14 @@ export default class BamRecord {
             let lref = 0;
             for (let c = 0; c < numCigarOps; ++c) {
                 const co = cigarView[c];
-                lref += (co >> 4) * ((CIGAR_CONSUMES_REF_MASK >> (co & 0xf)) & 1);
+                lref += (co >>> 4) * ((CIGAR_CONSUMES_REF_MASK >> (co & 0xf)) & 1);
             }
             return lref;
         }
         let lref = 0;
         for (let c = 0; c < numCigarOps; ++c) {
             const co = this._dataView.getInt32(p + c * 4, true);
-            lref += (co >> 4) * ((CIGAR_CONSUMES_REF_MASK >> (co & 0xf)) & 1);
+            lref += (co >>> 4) * ((CIGAR_CONSUMES_REF_MASK >> (co & 0xf)) & 1);
         }
         return lref;
     }
@@ -647,10 +656,10 @@ export default class BamRecord {
         const numCigarOps = flag_nc & 0xffff;
         const p = this.b0 + this.read_name_length;
         if (this._isCGTagPattern(p, numCigarOps)) {
-            // getTag, not this.tags: the real CIGAR lives in one tag, so there's no
-            // reason to decode every other tag on the record to reach it
-            const cg = this.getTag('CG');
-            return isNumericCigar(cg) ? cg : new Uint32Array(0);
+            const cg = this._findTag('CG', false);
+            if (isNumericCigar(cg)) {
+                return cg;
+            }
         }
         const absOffset = this._byteArray.byteOffset + p;
         if (absOffset % 4 === 0 && numCigarOps > 50) {
@@ -692,16 +701,19 @@ export default class BamRecord {
         let result = '';
         for (let i = 0, l = numeric.length; i < l; i++) {
             const packed = numeric[i];
-            result += packed >> 4;
+            result += packed >>> 4;
             result += String.fromCharCode(ASCII_CIGAR_CODES[packed & 0xf]);
         }
         return result;
     }
     get num_cigar_ops() {
-        return this.flag_nc & 0xffff;
+        return this._hasCGPlaceholder()
+            ? this.NUMERIC_CIGAR.length
+            : this.flag_nc & 0xffff;
     }
+    // the stored CIGAR field, which for a long CIGAR is the two-op placeholder
     get num_cigar_bytes() {
-        return this.num_cigar_ops << 2;
+        return (this.flag_nc & 0xffff) << 2;
     }
     get read_name_length() {
         return this.bin_mq_nl & 0xff;

package/esm/record.js.map CHANGED Viewed

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

@@ -1,7 +1,7 @@
 import { MAX_BGZF_BLOCK_SIZE, scanBgzfBlocks, unzip, } from '@gmod/bgzf-filehandle';
 import BAMFeature from "./record.js";
 import { parseHeaderText } from "./sam.js";
-import { BAM_MAGIC, concatUint8Array, parseRefSeqs, resolveFilehandle, throwIfAborted, } from "./util.js";
+import { BAM_MAGIC, concatUint8Array, decodeHeaderText, parseRefSeqs, readBlockSize, resolveFilehandle, throwIfAborted, } from "./util.js";
 /** compressed bytes per read; ~15 BGZF blocks, so ~8MB decompressed */
 const DEFAULT_WINDOW_SIZE = 1 << 20;
 /**
@@ -164,7 +164,7 @@ export async function* streamBamRecords({ bamFilehandle, bamPath, bamUrl, record
                     recordCarry = bytes;
                     continue;
                 }
-                const headerText = new TextDecoder('utf8').decode(bytes.subarray(8, 8 + lText));
+                const headerText = decodeHeaderText(bytes, lText);
                 onHeader?.({
                     headerText,
                     samHeader: parseHeaderText(headerText),
@@ -176,7 +176,7 @@ export async function* streamBamRecords({ bamFilehandle, bamPath, bamUrl, record
             }
             const sink = [];
             while (blockStart + 4 <= bytes.length) {
-                const blockSize = dataView.getInt32(blockStart, true);
+                const blockSize = readBlockSize(dataView, blockStart);
                 const blockEnd = blockStart + 4 + blockSize - 1;
                 if (blockEnd >= bytes.length) {
                     break;
@@ -189,12 +189,13 @@ export async function* streamBamRecords({ bamFilehandle, bamPath, bamUrl, record
                 // the window size, so it is as stable as a virtual offset without
                 // pretending to be one.
                 //
-                // NOT the crc32 of the record bytes that readBamFeatures falls back
-                // to when it has no positions. That is a content hash, so the two
-                // byte-identical records in exact_duplicate.bam collide on it, and
-                // hashing every record costs ~40% of the walk (135ms of 340ms over
-                // out.bam) where a counter costs nothing. The fallback only fires on
-                // an unusual path there; here it would fire on every record.
+                // NOT the hash of the record bytes that readBamFeatures falls back
+                // to when it has no positions: the two byte-identical records in
+                // exact_duplicate.bam collide on any content hash, and hashing
+                // every record cost ~40% of the walk (135ms of 340ms over out.bam,
+                // measured with crc32) where a counter costs nothing. The fallback
+                // only fires on an unusual path there; here it would fire on every
+                // record.
                 recordIndex++, dataView));
                 blockStart = blockEnd + 1;
             }

package/esm/streamBam.js.map CHANGED Viewed

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

@@ -4,6 +4,22 @@ import type { OffsetCoords } from './virtualOffset.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
 /** 'BAM\1' read as a little-endian int32 */
 export declare const BAM_MAGIC = 21840194;
+/**
+ * The `block_size` of the record at `offset`, rejecting one too small to hold a
+ * record's 32 bytes of fixed fields, as htslib's `bam_read1` does. A negative
+ * one would otherwise leave the loops that advance by it standing still,
+ * pushing a record per turn until the process runs out of memory.
+ */
+export declare function readBlockSize(dataView: DataView, offset: number): number;
+/**
+ * A 53-bit hash of `bytes[start, end)`: cyrb53 (public domain), taken over
+ * bytes. The id of a record read with no file positions, which has to be the
+ * same for the same record in every query, so it hashes content. It is 53 bits
+ * rather than crc32's 32 because ids are deduplicated: at 32 bits a fetch of
+ * 150,000 records expects about 2.6 distinct pairs to collide, each silently
+ * dropping a read, where 53 bits expect about 1e-6.
+ */
+export declare function contentHash53(bytes: Uint8Array, start: number, end: number): number;
 export declare function resolveFilehandle(filehandle?: GenericFilehandle, path?: string, url?: string): GenericFilehandle | undefined;
 export interface BamOpts {
     viewAsPairs?: boolean;
@@ -37,10 +53,13 @@ export declare const MAX_CONCURRENT_CHUNK_READS = 6;
  *
  * `blocksForRange` returns every chunk of every bin overlapping the query, at
  * every level of the binning scheme, minus the ones the linear index puts
- * entirely before it. On a long-read file that is wildly more than the query
- * reads: a coarse bin's chunks run to the end of the bin's span, so a 380bp
- * window on a deep ONT BAM resolves to 90 chunks / 43.5MB, of which
- * `getRecordsForRange` reads 6 / 7.8MB before the early stop fires.
+ * entirely before it. Until `max_off` (ADR 0023) also dropped the ones past it,
+ * that was wildly more than a long-read query reads: a coarse bin's chunks run
+ * to the end of the bin's span, so a 380bp window on a deep ONT BAM resolved to
+ * 90 chunks / 43.5MB, of which `getRecordsForRange` read 6 / 7.8MB before the
+ * early stop fired. Since then this changes the forecast in 4 of 320 fixture
+ * windows, undershooting in all 4; ADR 0023 says what to check before
+ * removing it.
  *
  * Two bounds, and the answer is the larger:
  *
@@ -84,6 +103,7 @@ export declare function parsePseudoBin(bytes: Uint8Array, offset: number): {
     lineCount: number;
 };
 export declare function clampChunkEnds(chunks: Chunk[], extraBoundaries?: ArrayLike<number>): void;
+export declare function decodeHeaderText(bytes: Uint8Array, lText: number): string;
 export declare function parseRefSeqs(uncba: Uint8Array, start: number, renameRefSeq: (s: string) => string): {
     chrToIndex: Record<string, number>;
     indexToChr: {

package/esm/util.js CHANGED Viewed

@@ -3,6 +3,41 @@ import Chunk from "./chunk.js";
 import { VirtualOffset } from "./virtualOffset.js";
 /** 'BAM\1' read as a little-endian int32 */
 export const BAM_MAGIC = 21840194;
+/**
+ * The `block_size` of the record at `offset`, rejecting one too small to hold a
+ * record's 32 bytes of fixed fields, as htslib's `bam_read1` does. A negative
+ * one would otherwise leave the loops that advance by it standing still,
+ * pushing a record per turn until the process runs out of memory.
+ */
+export function readBlockSize(dataView, offset) {
+    const blockSize = dataView.getInt32(offset, true);
+    if (blockSize < 32) {
+        throw new Error(`corrupt BAM record: block_size ${blockSize} at byte ${offset}`);
+    }
+    return blockSize;
+}
+/**
+ * A 53-bit hash of `bytes[start, end)`: cyrb53 (public domain), taken over
+ * bytes. The id of a record read with no file positions, which has to be the
+ * same for the same record in every query, so it hashes content. It is 53 bits
+ * rather than crc32's 32 because ids are deduplicated: at 32 bits a fetch of
+ * 150,000 records expects about 2.6 distinct pairs to collide, each silently
+ * dropping a read, where 53 bits expect about 1e-6.
+ */
+export function contentHash53(bytes, start, end) {
+    let h1 = 0xdeadbeef;
+    let h2 = 0x41c6ce57;
+    for (let i = start; i < end; i++) {
+        const b = bytes[i];
+        h1 = Math.imul(h1 ^ b, 2654435761);
+        h2 = Math.imul(h2 ^ b, 1597334677);
+    }
+    h1 = Math.imul(h1 ^ (h1 >>> 16), 2246822507);
+    h1 ^= Math.imul(h2 ^ (h2 >>> 13), 3266489909);
+    h2 = Math.imul(h2 ^ (h2 >>> 16), 2246822507);
+    h2 ^= Math.imul(h1 ^ (h1 >>> 13), 3266489909);
+    return 4294967296 * (2097151 & h2) + (h1 >>> 0);
+}
 export function resolveFilehandle(filehandle, path, url) {
     return (filehandle ??
         (path ? new LocalFile(path) : url ? new RemoteFile(url) : undefined));
@@ -25,10 +60,13 @@ export const MAX_CONCURRENT_CHUNK_READS = 6;
  *
  * `blocksForRange` returns every chunk of every bin overlapping the query, at
  * every level of the binning scheme, minus the ones the linear index puts
- * entirely before it. On a long-read file that is wildly more than the query
- * reads: a coarse bin's chunks run to the end of the bin's span, so a 380bp
- * window on a deep ONT BAM resolves to 90 chunks / 43.5MB, of which
- * `getRecordsForRange` reads 6 / 7.8MB before the early stop fires.
+ * entirely before it. Until `max_off` (ADR 0023) also dropped the ones past it,
+ * that was wildly more than a long-read query reads: a coarse bin's chunks run
+ * to the end of the bin's span, so a 380bp window on a deep ONT BAM resolved to
+ * 90 chunks / 43.5MB, of which `getRecordsForRange` read 6 / 7.8MB before the
+ * early stop fired. Since then this changes the forecast in 4 of 320 fixture
+ * windows, undershooting in all 4; ADR 0023 says what to check before
+ * removing it.
  *
  * Two bounds, and the answer is the larger:
  *
@@ -251,6 +289,13 @@ export function clampChunkEnds(chunks, extraBoundaries = []) {
         }
     }
 }
+// SAMv1 §4.2 counts NUL padding in l_text, and htslib reads the text as a C
+// string, so the header ends at the first NUL.
+export function decodeHeaderText(bytes, lText) {
+    const text = bytes.subarray(8, 8 + lText);
+    const nul = text.indexOf(0);
+    return new TextDecoder('utf8').decode(nul === -1 ? text : text.subarray(0, nul));
+}
 // Parse the BAM reference-sequence table (SAMv1.pdf §4.2). Returns undefined
 // if `uncba` doesn't yet contain the full table — caller fetches more bytes
 // and retries.