npm - @gmod/bam - Versions diffs - 7.8.0 → 7.8.2 - Mend

@gmod/bam 7.8.0 → 7.8.2

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 (11) hide show

package/dist/record.js CHANGED Viewed

@@ -83,9 +83,20 @@ function decodeTagString(ba, start, end) {
     }
     return textDecoder.decode(ba.subarray(start, end));
 }
-// Bitmask for ops that consume ref: M=0, D=2, N=3, P=6, ==7, X=8
-// Binary: 0b111001101 = 0x1CD
-const CIGAR_CONSUMES_REF_MASK = 0x1cd;
+// Bitmask for ops that consume ref: M=0, D=2, N=3, ==7, X=8
+// Binary: 0b110001101 = 0x18D
+//
+// P (=6) is NOT among them. Padding is a silent placeholder against a padded
+// reference and advances neither query nor reference, which is what htslib's
+// bam_cigar_type(P) == 0 says. Including it made every read carrying a P op
+// report an end one base per padded base too far.
+//
+// That said: nobody cares about P. Padded alignments come out of a handful of
+// assembly tools and are effectively absent from real BAMs — this was fixed
+// because it disagreed with htslib, not because it was hurting anyone. It is
+// covered incidentally by samspec.bam in the samtools agreement suite, and
+// that is enough; don't spend a dedicated fixture or test on it.
+const CIGAR_CONSUMES_REF_MASK = 0x18d;
 function isNumericCigar(value) {
     return (value instanceof Uint32Array ||
         value instanceof Int32Array ||

package/dist/record.js.map CHANGED Viewed

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

@@ -54,6 +54,14 @@ function optimizeChunks(chunks, lowest) {
         const chunkMaxBlock = chunk.maxv.blockPosition;
         // Merge if chunks are close enough: small gap between them, and the
         // combined span is bounded so we don't grow a single chunk indefinitely.
+        //
+        // Both constants were swept before being left alone — see ADR 0011.
+        // Dropping merging entirely, on the theory that a caller with a coalescing
+        // range cache makes it redundant, is much worse: a bare consumer goes from
+        // 6 reads to 95-378 on the same queries AND downloads MORE, because every
+        // small chunk pays its own tail padding where a merged one amortizes it.
+        // Raising the gap is worse too, partly because it blunts the early stop in
+        // _fetchChunkFeatures. Records are identical either way; only the I/O moves.
         if (chunkMinBlock - lastMaxBlock < 65000 &&
             chunkMaxBlock - lastMinBlock < 5000000) {
             const lastChunk = mergedChunks[mergedChunks.length - 1];
@@ -70,7 +78,47 @@ function optimizeChunks(chunks, lowest) {
             lastMaxBlock = chunkMaxBlock;
         }
     }
-    return mergedChunks;
+    return makeDisjoint(mergedChunks);
+}
+/**
+ * Trim any chunk that starts before its predecessor ends, so the spans a query
+ * reads never overlap.
+ *
+ * Merging alone does not guarantee this. Two chunks from different bins can
+ * overlap inside a single BGZF block while the merge above still declines to
+ * join them, because the combined span would exceed its 5MB cap — on
+ * test/data/out.bam that leaves `3804:0-4977599:16404` next to
+ * `4977599:5843-9719917:27612`, whose 10561 shared bytes of block 4977599 get
+ * fetched, decompressed and decoded by both. Every record in the overlap is
+ * then returned TWICE from getRecordsForRange (5 of out.bam's 6551), which a
+ * consumer sees as a duplicated read: rendered twice, counted twice in
+ * coverage, and colliding on any id derived from fileOffset.
+ *
+ * Safe because a BAI chunk's `maxv` is the virtual offset just past its last
+ * record — a record boundary — so no record begins inside the trimmed span and
+ * the union of the chunks is unchanged. Verified by record counts: the
+ * duplicates disappear and the number of DISTINCT records is identical.
+ */
+function makeDisjoint(chunks) {
+    const out = [chunks[0]];
+    for (let i = 1; i < chunks.length; i++) {
+        const chunk = chunks[i];
+        const prevMax = out[out.length - 1].maxv;
+        const cmp = chunk.minv.blockPosition - prevMax.blockPosition ||
+            chunk.minv.dataPosition - prevMax.dataPosition;
+        if (cmp >= 0) {
+            out.push(chunk);
+            continue;
+        }
+        // starts inside the previous chunk: begin where that one ended, and drop it
+        // entirely if that leaves nothing
+        const stillHasData = chunk.maxv.blockPosition - prevMax.blockPosition ||
+            chunk.maxv.dataPosition - prevMax.dataPosition;
+        if (stillHasData > 0) {
+            out.push(new chunk_ts_1.default(prevMax, chunk.maxv, chunk.bin, chunk.endPosition));
+        }
+    }
+    return out;
 }
 // The pseudo-bin's mapped-record count, a little-endian uint64. Read as two
 // 32-bit halves rather than via BigInt: exact up to Number.MAX_SAFE_INTEGER,
@@ -246,10 +294,22 @@ function concatUint8Array(args) {
     }
     return mergedArray;
 }
+// The end htslib's bam_endpos() reports: a record consuming no reference —
+// an unmapped mate placed at its mate's coordinate, or an empty CIGAR — still
+// covers one base rather than none, so it can be found by a query on the base
+// it sits at.
+function endpos(r) {
+    return r.end > r.start ? r.end : r.start + 1;
+}
 // Append records overlapping [min, max) on `chrId` into `out` (or a fresh
 // array if omitted). Records are assumed coordinate-sorted (by ref_id, then
 // start), so we stop scanning once we pass `max` within `chrId` or move past
 // `chrId` entirely. Returns the populated array.
+//
+// `end` is exclusive, so overlap is `end > min`, not `end >= min`: a read
+// finishing exactly where the query begins shares no base with it. samtools
+// agrees — `samtools view f.bam chr:124001-124300` omits a 150M read at
+// 1-based POS 123851, which ends at 124000.
 function appendInRange(records, chrId, min, max, out = []) {
     for (let i = 0, l = records.length; i < l; i++) {
         const r = records[i];
@@ -257,7 +317,7 @@ function appendInRange(records, chrId, min, max, out = []) {
             if (r.start >= max) {
                 break;
             }
-            else if (r.end >= min) {
+            else if (endpos(r) > min) {
                 out.push(r);
             }
         }

package/dist/util.js.map CHANGED Viewed

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

@@ -78,9 +78,20 @@ function decodeTagString(ba, start, end) {
     }
     return textDecoder.decode(ba.subarray(start, end));
 }
-// Bitmask for ops that consume ref: M=0, D=2, N=3, P=6, ==7, X=8
-// Binary: 0b111001101 = 0x1CD
-const CIGAR_CONSUMES_REF_MASK = 0x1cd;
+// Bitmask for ops that consume ref: M=0, D=2, N=3, ==7, X=8
+// Binary: 0b110001101 = 0x18D
+//
+// P (=6) is NOT among them. Padding is a silent placeholder against a padded
+// reference and advances neither query nor reference, which is what htslib's
+// bam_cigar_type(P) == 0 says. Including it made every read carrying a P op
+// report an end one base per padded base too far.
+//
+// That said: nobody cares about P. Padded alignments come out of a handful of
+// assembly tools and are effectively absent from real BAMs — this was fixed
+// because it disagreed with htslib, not because it was hurting anyone. It is
+// covered incidentally by samspec.bam in the samtools agreement suite, and
+// that is enough; don't spend a dedicated fixture or test on it.
+const CIGAR_CONSUMES_REF_MASK = 0x18d;
 function isNumericCigar(value) {
     return (value instanceof Uint32Array ||
         value instanceof Int32Array ||

package/esm/record.js.map CHANGED Viewed

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

@@ -41,6 +41,14 @@ export function optimizeChunks(chunks, lowest) {
         const chunkMaxBlock = chunk.maxv.blockPosition;
         // Merge if chunks are close enough: small gap between them, and the
         // combined span is bounded so we don't grow a single chunk indefinitely.
+        //
+        // Both constants were swept before being left alone — see ADR 0011.
+        // Dropping merging entirely, on the theory that a caller with a coalescing
+        // range cache makes it redundant, is much worse: a bare consumer goes from
+        // 6 reads to 95-378 on the same queries AND downloads MORE, because every
+        // small chunk pays its own tail padding where a merged one amortizes it.
+        // Raising the gap is worse too, partly because it blunts the early stop in
+        // _fetchChunkFeatures. Records are identical either way; only the I/O moves.
         if (chunkMinBlock - lastMaxBlock < 65000 &&
             chunkMaxBlock - lastMinBlock < 5000000) {
             const lastChunk = mergedChunks[mergedChunks.length - 1];
@@ -57,7 +65,47 @@ export function optimizeChunks(chunks, lowest) {
             lastMaxBlock = chunkMaxBlock;
         }
     }
-    return mergedChunks;
+    return makeDisjoint(mergedChunks);
+}
+/**
+ * Trim any chunk that starts before its predecessor ends, so the spans a query
+ * reads never overlap.
+ *
+ * Merging alone does not guarantee this. Two chunks from different bins can
+ * overlap inside a single BGZF block while the merge above still declines to
+ * join them, because the combined span would exceed its 5MB cap — on
+ * test/data/out.bam that leaves `3804:0-4977599:16404` next to
+ * `4977599:5843-9719917:27612`, whose 10561 shared bytes of block 4977599 get
+ * fetched, decompressed and decoded by both. Every record in the overlap is
+ * then returned TWICE from getRecordsForRange (5 of out.bam's 6551), which a
+ * consumer sees as a duplicated read: rendered twice, counted twice in
+ * coverage, and colliding on any id derived from fileOffset.
+ *
+ * Safe because a BAI chunk's `maxv` is the virtual offset just past its last
+ * record — a record boundary — so no record begins inside the trimmed span and
+ * the union of the chunks is unchanged. Verified by record counts: the
+ * duplicates disappear and the number of DISTINCT records is identical.
+ */
+function makeDisjoint(chunks) {
+    const out = [chunks[0]];
+    for (let i = 1; i < chunks.length; i++) {
+        const chunk = chunks[i];
+        const prevMax = out[out.length - 1].maxv;
+        const cmp = chunk.minv.blockPosition - prevMax.blockPosition ||
+            chunk.minv.dataPosition - prevMax.dataPosition;
+        if (cmp >= 0) {
+            out.push(chunk);
+            continue;
+        }
+        // starts inside the previous chunk: begin where that one ended, and drop it
+        // entirely if that leaves nothing
+        const stillHasData = chunk.maxv.blockPosition - prevMax.blockPosition ||
+            chunk.maxv.dataPosition - prevMax.dataPosition;
+        if (stillHasData > 0) {
+            out.push(new Chunk(prevMax, chunk.maxv, chunk.bin, chunk.endPosition));
+        }
+    }
+    return out;
 }
 // The pseudo-bin's mapped-record count, a little-endian uint64. Read as two
 // 32-bit halves rather than via BigInt: exact up to Number.MAX_SAFE_INTEGER,
@@ -233,10 +281,22 @@ export function concatUint8Array(args) {
     }
     return mergedArray;
 }
+// The end htslib's bam_endpos() reports: a record consuming no reference —
+// an unmapped mate placed at its mate's coordinate, or an empty CIGAR — still
+// covers one base rather than none, so it can be found by a query on the base
+// it sits at.
+function endpos(r) {
+    return r.end > r.start ? r.end : r.start + 1;
+}
 // Append records overlapping [min, max) on `chrId` into `out` (or a fresh
 // array if omitted). Records are assumed coordinate-sorted (by ref_id, then
 // start), so we stop scanning once we pass `max` within `chrId` or move past
 // `chrId` entirely. Returns the populated array.
+//
+// `end` is exclusive, so overlap is `end > min`, not `end >= min`: a read
+// finishing exactly where the query begins shares no base with it. samtools
+// agrees — `samtools view f.bam chr:124001-124300` omits a 150M read at
+// 1-based POS 123851, which ends at 124000.
 export function appendInRange(records, chrId, min, max, out = []) {
     for (let i = 0, l = records.length; i < l; i++) {
         const r = records[i];
@@ -244,7 +304,7 @@ export function appendInRange(records, chrId, min, max, out = []) {
             if (r.start >= max) {
                 break;
             }
-            else if (r.end >= min) {
+            else if (endpos(r) > min) {
                 out.push(r);
             }
         }

package/esm/util.js.map CHANGED Viewed

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

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "7.8.0",
+  "version": "7.8.2",
   "packageManager": "pnpm@11.15.1",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",

package/src/record.ts CHANGED Viewed

@@ -87,9 +87,20 @@ function decodeTagString(ba: Uint8Array, start: number, end: number) {
   return textDecoder.decode(ba.subarray(start, end))
 }
-// Bitmask for ops that consume ref: M=0, D=2, N=3, P=6, ==7, X=8
-// Binary: 0b111001101 = 0x1CD
-const CIGAR_CONSUMES_REF_MASK = 0x1cd
+// Bitmask for ops that consume ref: M=0, D=2, N=3, ==7, X=8
+// Binary: 0b110001101 = 0x18D
+//
+// P (=6) is NOT among them. Padding is a silent placeholder against a padded
+// reference and advances neither query nor reference, which is what htslib's
+// bam_cigar_type(P) == 0 says. Including it made every read carrying a P op
+// report an end one base per padded base too far.
+//
+// That said: nobody cares about P. Padded alignments come out of a handful of
+// assembly tools and are effectively absent from real BAMs — this was fixed
+// because it disagreed with htslib, not because it was hurting anyone. It is
+// covered incidentally by samspec.bam in the samtools agreement suite, and
+// that is enough; don't spend a dedicated fixture or test on it.
+const CIGAR_CONSUMES_REF_MASK = 0x18d
 // A CIGAR as packed op words. Either a view over (or copy of) the record's own
 // CIGAR field, or the CG tag's array for long-CIGAR records — hence Int32Array

package/src/util.ts CHANGED Viewed

@@ -74,6 +74,14 @@ export function optimizeChunks(chunks: Chunk[], lowest?: OffsetCoords) {
     const chunkMaxBlock = chunk.maxv.blockPosition
     // Merge if chunks are close enough: small gap between them, and the
     // combined span is bounded so we don't grow a single chunk indefinitely.
+    //
+    // Both constants were swept before being left alone — see ADR 0011.
+    // Dropping merging entirely, on the theory that a caller with a coalescing
+    // range cache makes it redundant, is much worse: a bare consumer goes from
+    // 6 reads to 95-378 on the same queries AND downloads MORE, because every
+    // small chunk pays its own tail padding where a merged one amortizes it.
+    // Raising the gap is worse too, partly because it blunts the early stop in
+    // _fetchChunkFeatures. Records are identical either way; only the I/O moves.
     if (
       chunkMinBlock - lastMaxBlock < 65000 &&
       chunkMaxBlock - lastMinBlock < 5000000
@@ -98,7 +106,50 @@ export function optimizeChunks(chunks: Chunk[], lowest?: OffsetCoords) {
     }
   }
-  return mergedChunks
+  return makeDisjoint(mergedChunks)
+}
+/**
+ * Trim any chunk that starts before its predecessor ends, so the spans a query
+ * reads never overlap.
+ *
+ * Merging alone does not guarantee this. Two chunks from different bins can
+ * overlap inside a single BGZF block while the merge above still declines to
+ * join them, because the combined span would exceed its 5MB cap — on
+ * test/data/out.bam that leaves `3804:0-4977599:16404` next to
+ * `4977599:5843-9719917:27612`, whose 10561 shared bytes of block 4977599 get
+ * fetched, decompressed and decoded by both. Every record in the overlap is
+ * then returned TWICE from getRecordsForRange (5 of out.bam's 6551), which a
+ * consumer sees as a duplicated read: rendered twice, counted twice in
+ * coverage, and colliding on any id derived from fileOffset.
+ *
+ * Safe because a BAI chunk's `maxv` is the virtual offset just past its last
+ * record — a record boundary — so no record begins inside the trimmed span and
+ * the union of the chunks is unchanged. Verified by record counts: the
+ * duplicates disappear and the number of DISTINCT records is identical.
+ */
+function makeDisjoint(chunks: Chunk[]) {
+  const out: Chunk[] = [chunks[0]!]
+  for (let i = 1; i < chunks.length; i++) {
+    const chunk = chunks[i]!
+    const prevMax = out[out.length - 1]!.maxv
+    const cmp =
+      chunk.minv.blockPosition - prevMax.blockPosition ||
+      chunk.minv.dataPosition - prevMax.dataPosition
+    if (cmp >= 0) {
+      out.push(chunk)
+      continue
+    }
+    // starts inside the previous chunk: begin where that one ended, and drop it
+    // entirely if that leaves nothing
+    const stillHasData =
+      chunk.maxv.blockPosition - prevMax.blockPosition ||
+      chunk.maxv.dataPosition - prevMax.dataPosition
+    if (stillHasData > 0) {
+      out.push(new Chunk(prevMax, chunk.maxv, chunk.bin, chunk.endPosition))
+    }
+  }
+  return out
 }
 // The pseudo-bin's mapped-record count, a little-endian uint64. Read as two
@@ -318,10 +369,23 @@ interface Positioned {
   end: number
 }
+// The end htslib's bam_endpos() reports: a record consuming no reference —
+// an unmapped mate placed at its mate's coordinate, or an empty CIGAR — still
+// covers one base rather than none, so it can be found by a query on the base
+// it sits at.
+function endpos(r: Positioned) {
+  return r.end > r.start ? r.end : r.start + 1
+}
 // Append records overlapping [min, max) on `chrId` into `out` (or a fresh
 // array if omitted). Records are assumed coordinate-sorted (by ref_id, then
 // start), so we stop scanning once we pass `max` within `chrId` or move past
 // `chrId` entirely. Returns the populated array.
+//
+// `end` is exclusive, so overlap is `end > min`, not `end >= min`: a read
+// finishing exactly where the query begins shares no base with it. samtools
+// agrees — `samtools view f.bam chr:124001-124300` omits a 150M read at
+// 1-based POS 123851, which ends at 124000.
 export function appendInRange<T extends Positioned>(
   records: T[],
   chrId: number,
@@ -334,7 +398,7 @@ export function appendInRange<T extends Positioned>(
     if (r.ref_id === chrId) {
       if (r.start >= max) {
         break
-      } else if (r.end >= min) {
+      } else if (endpos(r) > min) {
         out.push(r)
       }
     } else if (r.ref_id > chrId) {