@gmod/bam 1.1.14 → 1.1.17

package/esm/csi.js

@@ -151,10 +151,7 @@ export default class CSI extends IndexFile {
             min = 0;
         }
         const indexData = await this.parse(opts);
-        if (!indexData) {
-            return [];
-        }
-        const ba = indexData.indices[refId];
+        const ba = indexData === null || indexData === void 0 ? void 0 : indexData.indices[refId];
         if (!ba) {
             return [];
         }
@@ -174,8 +171,8 @@ export default class CSI extends IndexFile {
         return optimizeChunks(chunks, new VirtualOffset(0, 0));
     }
     /**
-     * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
-     * @returns {Array[number]}
+     * calculate the list of bins that may overlap with region [beg,end)
+     * (zero-based half-open)
      */
     reg2bins(beg, end) {
         beg -= 1; // < convert to 1-based closed

package/esm/csi.js.map

@@ -1 +1 @@
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+{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,MAAM,CAAA;AACvB,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,aAAa,EAAE,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAC1D,OAAO,KAAK,MAAM,SAAS,CAAA;AAC3B,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,cAAc,EAAY,MAAM,QAAQ,CAAA;AAEhF,OAAO,SAAS,MAAM,aAAa,CAAA;AAEnC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAS;IAIxC,YAAY,IAAS;QACnB,KAAK,CAAC,IAAI,CAAC,CAAA;QACX,IAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACrB,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACd,IAAI,CAAC,QAAQ,GAAG,CAAC,CAAA;IACnB,CAAC;IACD,KAAK,CAAC,SAAS,CAAC,KAAa;QAC3B,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACpC,IAAI,CAAC,SAAS,EAAE;YACd,OAAO,CAAC,CAAC,CAAA;SACV;QACD,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACpC,IAAI,CAAC,GAAG,EAAE;YACR,OAAO,CAAC,CAAC,CAAA;SACV;QACD,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAC1C,IAAI,KAAK,EAAE;YACT,OAAO,KAAK,CAAC,SAAS,CAAA;SACvB;QACD,OAAO,CAAC,CAAC,CAAA;IACX,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,OAAO,EAAE,CAAA;IACX,CAAC;IAED,YAAY,CAAC,KAAa,EAAE,MAAc,EAAE,SAAiB;QAC3D,IAAI,SAAS,GAAG,EAAE,EAAE;YAClB,OAAO,EAAE,CAAA;SACV;QAED,MAAM,IAAI,GAA2B,EAAE,CAAA;QACvC,IAAI,CAAC,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QAC5C,IAAI,CAAC,cAAc;YACjB,IAAI,CAAC,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACxE,IAAI,CAAC,MAAM,GACT,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAGnC,CAAC,IAAI,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACzB,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,qCAAqC,IAAI,CAAC,WAAW,EAAE,CAAC,CAAA;SACzE;QACD,IAAI,CAAC,aAAa,GAAG;YACnB,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YAClC,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YACpC,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC;SACpC,CAAA;QACD,IAAI,CAAC,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAC/C,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QACzE,IAAI,CAAC,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAC/C,MAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAExD,MAAM,CAAC,MAAM,CACX,IAAI,EACJ,IAAI,CAAC,eAAe,CAClB,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,CAC7D,CACF,CAAA;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,eAAe,CAAC,UAAkB;QAChC,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,aAAa,GAAG,CAAC,CAAA;QACrB,MAAM,WAAW,GAAG,EAAE,CAAA;QACtB,MAAM,WAAW,GAA8B,EAAE,CAAA;QACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC7C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE;gBAClB,IAAI,aAAa,GAAG,CAAC,EAAE;oBACrB,IAAI,OAAO,GAAG,UAAU,CAAC,QAAQ,CAAC,MAAM,EAAE,aAAa,EAAE,CAAC,CAAC,CAAA;oBAC3D,OAAO,GAAG,IAAI,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;oBACpC,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;oBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;iBACjC;gBACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;gBACrB,SAAS,IAAI,CAAC,CAAA;aACf;SACF;QACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;IACrC,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM,CAAC,IAA8B;QACzC,MAAM,IAAI,GAA2B,EAAE,GAAG,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,IAAI,EAAE,EAAE,CAAA;QACzE,MAAM,MAAM,GAAG,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAW,CAAA;QAC/D,MAAM,KAAK,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC,CAAA;QAEjC,0BAA0B;QAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;YACxC,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA;SACpB;aAAM,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;YAC/C,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA;SACpB;aAAM;YACL,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;YACjC,oDAAoD;SACrD;QAED,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACpC,IAAI,CAAC,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACjC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAC3D,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;QACvC,IAAI,SAAS,EAAE;YACb,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,EAAE,SAAS,CAAC,CAAC,CAAA;SAC7D;QACD,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,GAAG,SAAS,CAAC,CAAA;QAEjD,+CAA+C;QAC/C,IAAI,CAAC,OAAO,GAAG,IAAI,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;QACvC,IAAI,UAAU,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;QACnC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;YACzC,MAAM,eAAe,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;YAClC,oBAAoB;YACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;YAC9C,UAAU,IAAI,CAAC,CAAA;YACf,MAAM,QAAQ,GAA+B,EAAE,CAAA;YAC/C,IAAI,KAAK,CAAA,CAAC,iDAAiD;YAC3D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;gBACpC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;gBAC1C,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE;oBAC3B,yDAAyD;oBACzD,qCAAqC;oBACrC,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;oBAClD,UAAU,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,EAAE,CAAA;iBAClC;qBAAM;oBACL,MAAM,OAA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package/esm/record.js

@@ -33,8 +33,7 @@ export default class BamRecord {
         return this._get(field.toLowerCase());
     }
     end() {
-        return (this.get('start') +
-            (this.get('length_on_ref') || this.get('seq_length') || undefined));
+        return this.get('start') + this.get('length_on_ref');
     }
     seq_id() {
         return this._refID;
@@ -419,9 +418,13 @@ export default class BamRecord {
     }
     _flags() { }
     length_on_ref() {
-        this.get('cigar'); // the length_on_ref is set as a
-        // side effect of the CIGAR parsing
-        return this.data.length_on_ref;
+        if (this.data.length_on_ref) {
+            return this.data.length_on_ref;
+        }
+        else {
+            this.get('cigar'); // the length_on_ref is set as a side effect
+            return this.data.length_on_ref;
+        }
     }
     _n_cigar_op() {
         return this.get('_flag_nc') & 0xffff;

package/esm/record.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "1.1.14",
+  "version": "1.1.17",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": "GMOD/bam-js",
@@ -16,7 +16,8 @@
   },
   "files": [
     "dist",
-    "esm"
+    "esm",
+    "src"
   ],
   "scripts": {
     "test": "jest",
@@ -38,30 +39,33 @@
     "genomics"
   ],
   "dependencies": {
-    "@gmod/bgzf-filehandle": "^1.3.3",
+    "@gmod/bgzf-filehandle": "^1.4.4",
+    "abortable-promise-cache": "^1.5.0",
     "buffer-crc32": "^0.2.13",
     "cross-fetch": "^3.0.2",
-    "generic-filehandle": "^2.0.0",
+    "generic-filehandle": "^3.0.0",
     "long": "^4.0.0",
-    "object.entries-ponyfill": "^1.0.1"
+    "object.entries-ponyfill": "^1.0.1",
+    "quick-lru": "^2.0.0"
   },
   "devDependencies": {
     "@types/buffer-crc32": "^0.2.0",
-    "@types/jest": "^27.4.1",
-    "@types/long": "^4.0.0",
-    "@types/node": "^17.0.21",
-    "@typescript-eslint/eslint-plugin": "^5.12.1",
-    "@typescript-eslint/parser": "^5.12.1",
-    "eslint": "^8.9.0",
-    "eslint-config-prettier": "^8.4.0",
-    "eslint-plugin-import": "^2.25.4",
-    "eslint-plugin-prettier": "^4.0.0",
-    "jest": "^27.5.1",
-    "prettier": "^2.4.1",
+    "@types/jest": "^28.1.6",
+    "@types/long": "^4.0.2",
+    "@types/node": "^18.0.6",
+    "@types/quick-lru": "^2.0.0",
+    "@typescript-eslint/eslint-plugin": "^5.30.7",
+    "@typescript-eslint/parser": "^5.30.7",
+    "eslint": "^8.20.0",
+    "eslint-config-prettier": "^8.5.0",
+    "eslint-plugin-import": "^2.26.0",
+    "eslint-plugin-prettier": "^4.2.1",
+    "jest": "^28.1.3",
+    "prettier": "^2.7.1",
     "rimraf": "^3.0.2",
     "standard-changelog": "^2.0.27",
-    "ts-jest": "^27.1.3",
-    "typescript": "^4.5.5"
+    "ts-jest": "^28.0.7",
+    "typescript": "^4.7.4"
   },
   "publishConfig": {
     "access": "public"

package/src/bai.ts

@@ -0,0 +1,227 @@
+import Long from 'long'
+import { fromBytes } from './virtualOffset'
+import Chunk from './chunk'
+
+import IndexFile from './indexFile'
+import { longToNumber, optimizeChunks, BaseOpts } from './util'
+
+const BAI_MAGIC = 21578050 // BAI\1
+
+function roundDown(n: number, multiple: number) {
+  return n - (n % multiple)
+}
+function roundUp(n: number, multiple: number) {
+  return n - (n % multiple) + multiple
+}
+
+export default class BAI extends IndexFile {
+  baiP?: Promise<Buffer>
+
+  parsePseudoBin(bytes: Buffer, offset: number) {
+    const lineCount = longToNumber(
+      Long.fromBytesLE(
+        Array.prototype.slice.call(bytes, offset + 16, offset + 24),
+        true,
+      ),
+    )
+    return { lineCount }
+  }
+
+  async lineCount(refId: number, opts: BaseOpts = {}) {
+    const prom = await this.parse(opts)
+    const index = prom.indices[refId]
+    if (!index) {
+      return -1
+    }
+    const ret = index.stats || {}
+    return ret.lineCount === undefined ? -1 : ret.lineCount
+  }
+
+  fetchBai(opts: BaseOpts = {}) {
+    if (!this.baiP) {
+      this.baiP = this.filehandle.readFile(opts).catch(e => {
+        this.baiP = undefined
+        throw e
+      }) as Promise<Buffer>
+    }
+    return this.baiP
+  }
+
+  // fetch and parse the index
+  async _parse() {
+    const data: { [key: string]: any } = { bai: true, maxBlockSize: 1 << 16 }
+    const bytes = await this.fetchBai()
+
+    // check BAI magic numbers
+    if (bytes.readUInt32LE(0) !== BAI_MAGIC) {
+      throw new Error('Not a BAI file')
+    }
+
+    data.refCount = bytes.readInt32LE(4)
+    const depth = 5
+    const binLimit = ((1 << ((depth + 1) * 3)) - 1) / 7
+
+    // read the indexes for each reference sequence
+    data.indices = new Array(data.refCount)
+    let currOffset = 8
+    for (let i = 0; i < data.refCount; i += 1) {
+      // the binning index
+      const binCount = bytes.readInt32LE(currOffset)
+      let stats
+
+      currOffset += 4
+      const binIndex: { [key: number]: Chunk[] } = {}
+      for (let j = 0; j < binCount; j += 1) {
+        const bin = bytes.readUInt32LE(currOffset)
+        currOffset += 4
+        if (bin === binLimit + 1) {
+          currOffset += 4
+          stats = this.parsePseudoBin(bytes, currOffset)
+          currOffset += 32
+        } else if (bin > binLimit + 1) {
+          throw new Error('bai index contains too many bins, please use CSI')
+        } else {
+          const chunkCount = bytes.readInt32LE(currOffset)
+          currOffset += 4
+          const chunks = new Array(chunkCount)
+          for (let k = 0; k < chunkCount; k += 1) {
+            const u = fromBytes(bytes, currOffset)
+            const v = fromBytes(bytes, currOffset + 8)
+            currOffset += 16
+            this._findFirstData(data, u)
+            chunks[k] = new Chunk(u, v, bin)
+          }
+          binIndex[bin] = chunks
+        }
+      }
+
+      const linearCount = bytes.readInt32LE(currOffset)
+      currOffset += 4
+      // as we're going through the linear index, figure out
+      // the smallest virtual offset in the indexes, which
+      // tells us where the BAM header ends
+      const linearIndex = new Array(linearCount)
+      for (let k = 0; k < linearCount; k += 1) {
+        linearIndex[k] = fromBytes(bytes, currOffset)
+        currOffset += 8
+        this._findFirstData(data, linearIndex[k])
+      }
+
+      data.indices[i] = { binIndex, linearIndex, stats }
+    }
+
+    return data
+  }
+
+  async indexCov(
+    seqId: number,
+    start?: number,
+    end?: number,
+    opts: BaseOpts = {},
+  ): Promise<{ start: number; end: number; score: number }[]> {
+    const v = 16384
+    const range = start !== undefined
+    const indexData = await this.parse(opts)
+    const seqIdx = indexData.indices[seqId]
+    if (!seqIdx) {
+      return []
+    }
+    const { linearIndex = [], stats } = seqIdx
+    if (!linearIndex.length) {
+      return []
+    }
+    const e = end !== undefined ? roundUp(end, v) : (linearIndex.length - 1) * v
+    const s = start !== undefined ? roundDown(start, v) : 0
+    let depths
+    if (range) {
+      depths = new Array((e - s) / v)
+    } else {
+      depths = new Array(linearIndex.length - 1)
+    }
+    const totalSize = linearIndex[linearIndex.length - 1].blockPosition
+    if (e > (linearIndex.length - 1) * v) {
+      throw new Error('query outside of range of linear index')
+    }
+    let currentPos = linearIndex[s / v].blockPosition
+    for (let i = s / v, j = 0; i < e / v; i++, j++) {
+      depths[j] = {
+        score: linearIndex[i + 1].blockPosition - currentPos,
+        start: i * v,
+        end: i * v + v,
+      }
+      currentPos = linearIndex[i + 1].blockPosition
+    }
+    return depths.map(d => {
+      return { ...d, score: (d.score * stats.lineCount) / totalSize }
+    })
+  }
+
+  /**
+   * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
+   * @returns {Array[number]}
+   */
+  reg2bins(beg: number, end: number) {
+    end -= 1
+    return [
+      [0, 0],
+      [1 + (beg >> 26), 1 + (end >> 26)],
+      [9 + (beg >> 23), 9 + (end >> 23)],
+      [73 + (beg >> 20), 73 + (end >> 20)],
+      [585 + (beg >> 17), 585 + (end >> 17)],
+      [4681 + (beg >> 14), 4681 + (end >> 14)],
+    ]
+  }
+
+  async blocksForRange(
+    refId: number,
+    min: number,
+    max: number,
+    opts: BaseOpts = {},
+  ) {
+    if (min < 0) {
+      min = 0
+    }
+
+    const indexData = await this.parse(opts)
+    if (!indexData) {
+      return []
+    }
+    const ba = indexData.indices[refId]
+    if (!ba) {
+      return []
+    }
+
+    // List of bin #s that overlap min, max
+    const overlappingBins = this.reg2bins(min, max)
+    const chunks: Chunk[] = []
+
+    // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
+    for (const [start, end] of overlappingBins) {
+      for (let bin = start; bin <= end; bin++) {
+        if (ba.binIndex[bin]) {
+          const binChunks = ba.binIndex[bin]
+          for (let c = 0; c < binChunks.length; ++c) {
+            chunks.push(new Chunk(binChunks[c].minv, binChunks[c].maxv, bin))
+          }
+        }
+      }
+    }
+
+    // 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 = null
+    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) {
+        if (!lowest || vp.compareTo(lowest) < 0) {
+          lowest = vp
+        }
+      }
+    }
+
+    return optimizeChunks(chunks, lowest)
+  }
+}