@gmod/bam 1.1.18 → 2.0.0

package/dist/bai.js

@@ -12,11 +12,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const long_1 = __importDefault(require("long"));
 const virtualOffset_1 = require("./virtualOffset");
 const chunk_1 = __importDefault(require("./chunk"));
-const indexFile_1 = __importDefault(require("./indexFile"));
 const util_1 = require("./util");
+const indexFile_1 = __importDefault(require("./indexFile"));
 const BAI_MAGIC = 21578050; // BAI\1
 function roundDown(n, multiple) {
     return n - (n % multiple);
@@ -24,91 +23,93 @@ function roundDown(n, multiple) {
 function roundUp(n, multiple) {
     return n - (n % multiple) + multiple;
 }
+function reg2bins(beg, end) {
+    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)],
+    ];
+}
 class BAI extends indexFile_1.default {
-    parsePseudoBin(bytes, offset) {
-        const lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(Array.prototype.slice.call(bytes, offset + 16, offset + 24), true));
-        return { lineCount };
-    }
-    lineCount(refId, opts = {}) {
+    lineCount(refId, opts) {
+        var _a, _b;
         return __awaiter(this, void 0, void 0, function* () {
-            const prom = yield this.parse(opts);
-            const index = prom.indices[refId];
-            if (!index) {
-                return -1;
-            }
-            const ret = index.stats || {};
-            return ret.lineCount === undefined ? -1 : ret.lineCount;
+            const indexData = yield this.parse(opts);
+            return ((_b = (_a = indexData.indices[refId]) === null || _a === void 0 ? void 0 : _a.stats) === null || _b === void 0 ? void 0 : _b.lineCount) || 0;
         });
     }
-    fetchBai(opts = {}) {
-        if (!this.baiP) {
-            this.baiP = this.filehandle.readFile(opts).catch(e => {
-                this.baiP = undefined;
-                throw e;
-            });
-        }
-        return this.baiP;
-    }
     // fetch and parse the index
-    _parse() {
+    _parse(opts) {
         return __awaiter(this, void 0, void 0, function* () {
-            const data = { bai: true, maxBlockSize: 1 << 16 };
-            const bytes = yield this.fetchBai();
+            const bytes = (yield this.filehandle.readFile(opts));
             // check BAI magic numbers
             if (bytes.readUInt32LE(0) !== BAI_MAGIC) {
                 throw new Error('Not a BAI file');
             }
-            data.refCount = bytes.readInt32LE(4);
+            const 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) {
+            let curr = 8;
+            let firstDataLine;
+            const indices = new Array(refCount);
+            for (let i = 0; i < refCount; i++) {
                 // the binning index
-                const binCount = bytes.readInt32LE(currOffset);
+                const binCount = bytes.readInt32LE(curr);
                 let stats;
-                currOffset += 4;
+                curr += 4;
                 const binIndex = {};
                 for (let j = 0; j < binCount; j += 1) {
-                    const bin = bytes.readUInt32LE(currOffset);
-                    currOffset += 4;
+                    const bin = bytes.readUInt32LE(curr);
+                    curr += 4;
                     if (bin === binLimit + 1) {
-                        currOffset += 4;
-                        stats = this.parsePseudoBin(bytes, currOffset);
-                        currOffset += 32;
+                        curr += 4;
+                        stats = (0, util_1.parsePseudoBin)(bytes, curr + 16);
+                        curr += 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 chunkCount = bytes.readInt32LE(curr);
+                        curr += 4;
                         const chunks = new Array(chunkCount);
-                        for (let k = 0; k < chunkCount; k += 1) {
-                            const u = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
-                            const v = (0, virtualOffset_1.fromBytes)(bytes, currOffset + 8);
-                            currOffset += 16;
-                            this._findFirstData(data, u);
+                        for (let k = 0; k < chunkCount; k++) {
+                            const u = (0, virtualOffset_1.fromBytes)(bytes, curr);
+                            curr += 8;
+                            const v = (0, virtualOffset_1.fromBytes)(bytes, curr);
+                            curr += 8;
+                            firstDataLine = (0, util_1.findFirstData)(firstDataLine, u);
                             chunks[k] = new chunk_1.default(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 linearCount = bytes.readInt32LE(curr);
+                curr += 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] = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
-                    currOffset += 8;
-                    this._findFirstData(data, linearIndex[k]);
+                for (let j = 0; j < linearCount; j++) {
+                    const offset = (0, virtualOffset_1.fromBytes)(bytes, curr);
+                    curr += 8;
+                    firstDataLine = (0, util_1.findFirstData)(firstDataLine, offset);
+                    linearIndex[j] = offset;
                 }
-                data.indices[i] = { binIndex, linearIndex, stats };
+                indices[i] = { binIndex, linearIndex, stats };
             }
-            return data;
+            return {
+                bai: true,
+                firstDataLine,
+                maxBlockSize: 1 << 16,
+                indices,
+                refCount,
+            };
         });
     }
     indexCov(seqId, start, end, opts = {}) {
@@ -121,18 +122,14 @@ class BAI extends indexFile_1.default {
                 return [];
             }
             const { linearIndex = [], stats } = seqIdx;
-            if (!linearIndex.length) {
+            if (linearIndex.length === 0) {
                 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 e = end === undefined ? (linearIndex.length - 1) * v : roundUp(end, v);
+            const s = start === undefined ? 0 : roundDown(start, v);
+            const depths = range
+                ? new Array((e - s) / v)
+                : 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');
@@ -146,26 +143,9 @@ class BAI extends indexFile_1.default {
                 };
                 currentPos = linearIndex[i + 1].blockPosition;
             }
-            return depths.map(d => {
-                return Object.assign(Object.assign({}, d), { score: (d.score * stats.lineCount) / totalSize });
-            });
+            return depths.map(d => (Object.assign(Object.assign({}, d), { score: (d.score * ((stats === null || stats === void 0 ? void 0 : stats.lineCount) || 0)) / totalSize })));
         });
     }
-    /**
-     * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
-     * @returns {Array[number]}
-     */
-    reg2bins(beg, end) {
-        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)],
-        ];
-    }
     blocksForRange(refId, min, max, opts = {}) {
         return __awaiter(this, void 0, void 0, function* () {
             if (min < 0) {
@@ -180,15 +160,15 @@ class BAI extends indexFile_1.default {
                 return [];
             }
             // List of bin #s that overlap min, max
-            const overlappingBins = this.reg2bins(min, max);
+            const overlappingBins = reg2bins(min, max);
             const chunks = [];
             // 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_1.default(binChunks[c].minv, binChunks[c].maxv, bin));
+                        for (const binChunk of binChunks) {
+                            chunks.push(binChunk);
                         }
                     }
                 }
@@ -196,20 +176,36 @@ class BAI extends indexFile_1.default {
             // 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;
+            let lowest;
             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;
-                    }
+                if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
+                    lowest = vp;
                 }
             }
             return (0, util_1.optimizeChunks)(chunks, lowest);
         });
     }
+    parse(opts = {}) {
+        return __awaiter(this, void 0, void 0, function* () {
+            if (!this.setupP) {
+                this.setupP = this._parse(opts).catch(e => {
+                    this.setupP = undefined;
+                    throw e;
+                });
+            }
+            return this.setupP;
+        });
+    }
+    hasRefSeq(seqId, opts = {}) {
+        var _a;
+        return __awaiter(this, void 0, void 0, function* () {
+            const header = yield this.parse(opts);
+            return !!((_a = header.indices[seqId]) === null || _a === void 0 ? void 0 : _a.binIndex);
+        });
+    }
 }
 exports.default = BAI;
 //# sourceMappingURL=bai.js.map

package/dist/bai.js.map

@@ -1 +1 @@
-{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":";;;;;;;;;;;;;;AAAA,gDAAuB;AACvB,mDAA2C;AAC3C,oDAA2B;AAE3B,4DAAmC;AACnC,iCAA+D;AAE/D,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEnC,SAAS,SAAS,CAAC,CAAS,EAAE,QAAgB;IAC5C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAA;AAC3B,CAAC;AACD,SAAS,OAAO,CAAC,CAAS,EAAE,QAAgB;IAC1C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,GAAG,QAAQ,CAAA;AACtC,CAAC;AAED,MAAqB,GAAI,SAAQ,mBAAS;IAGxC,cAAc,CAAC,KAAa,EAAE,MAAc;QAC1C,MAAM,SAAS,GAAG,IAAA,mBAAY,EAC5B,cAAI,CAAC,WAAW,CACd,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,EAAE,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,CAAC,EAC3D,IAAI,CACL,CACF,CAAA;QACD,OAAO,EAAE,SAAS,EAAE,CAAA;IACtB,CAAC;IAEK,SAAS,CAAC,KAAa,EAAE,OAAiB,EAAE;;YAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACnC,MAAM,KAAK,GAAG,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YACjC,IAAI,CAAC,KAAK,EAAE;gBACV,OAAO,CAAC,CAAC,CAAA;aACV;YACD,MAAM,GAAG,GAAG,KAAK,CAAC,KAAK,IAAI,EAAE,CAAA;YAC7B,OAAO,GAAG,CAAC,SAAS,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,SAAS,CAAA;QACzD,CAAC;KAAA;IAED,QAAQ,CAAC,OAAiB,EAAE;QAC1B,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE;YACd,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACnD,IAAI,CAAC,IAAI,GAAG,SAAS,CAAA;gBACrB,MAAM,CAAC,CAAA;YACT,CAAC,CAAoB,CAAA;SACtB;QACD,OAAO,IAAI,CAAC,IAAI,CAAA;IAClB,CAAC;IAED,4BAA4B;IACtB,MAAM;;YACV,MAAM,IAAI,GAA2B,EAAE,GAAG,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,IAAI,EAAE,EAAE,CAAA;YACzE,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;YAEnC,0BAA0B;YAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE;gBACvC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;aAClC;YAED,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACpC,MAAM,KAAK,GAAG,CAAC,CAAA;YACf,MAAM,QAAQ,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;YAEnD,+CAA+C;YAC/C,IAAI,CAAC,OAAO,GAAG,IAAI,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;YACvC,IAAI,UAAU,GAAG,CAAC,CAAA;YAClB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;gBACzC,oBAAoB;gBACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;gBAC9C,IAAI,KAAK,CAAA;gBAET,UAAU,IAAI,CAAC,CAAA;gBACf,MAAM,QAAQ,GAA+B,EAAE,CAAA;gBAC/C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;oBACpC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;oBAC1C,UAAU,IAAI,CAAC,CAAA;oBACf,IAAI,GAAG,KAAK,QAAQ,GAAG,CAAC,EAAE;wBACxB,UAAU,IAAI,CAAC,CAAA;wBACf,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;wBAC9C,UAAU,IAAI,EAAE,CAAA;qBACjB;yBAAM,IAAI,GAAG,GAAG,QAAQ,GAAG,CAAC,EAAE;wBAC7B,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;qBACpE;yBAAM;wBACL,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;wBAChD,UAAU,IAAI,CAAC,CAAA;wBACf,MAAM,MAAM,GAAG,IAAI,KAAK,CAAC,UAAU,CAAC,CAAA;wBACpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE;4BACtC,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,CAAC,CAAA;4BACtC,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;4BAC1C,UAAU,IAAI,EAAE,CAAA;4BAChB,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,CAAC,CAAC,CAAA;4BAC5B,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,eAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;yBACjC;wBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;qBACvB;iBACF;gBAED,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;gBACjD,UAAU,IAAI,CAAC,CAAA;gBACf,sDAAsD;gBACtD,oDAAoD;gBACpD,qCAAqC;gBACrC,MAAM,WAAW,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,CAAA;gBAC1C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE;oBACvC,WAAW,CAAC,CAAC,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,CAAC,CAAA;oBAC7C,UAAU,IAAI,CAAC,CAAA;oBACf,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,WAAW,CAAC,CAAC,CAAC,CAAC,CAAA;iBAC1C;gBAED,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,CAAA;aACnD;YAED,OAAO,IAAI,CAAA;QACb,CAAC;KAAA;IAEK,QAAQ,CACZ,KAAa,EACb,KAAc,EACd,GAAY,EACZ,OAAiB,EAAE;;YAEnB,MAAM,CAAC,GAAG,KAAK,CAAA;YACf,MAAM,KAAK,GAAG,KAAK,KAAK,SAAS,CAAA;YACjC,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,MAAM,MAAM,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YACvC,IAAI,CAAC,MAAM,EAAE;gBACX,OAAO,EAAE,CAAA;aACV;YACD,MAAM,EAAE,WAAW,GAAG,EAAE,EAAE,KAAK,EAAE,GAAG,MAAM,CAAA;YAC1C,IAAI,CAAC,WAAW,CAAC,MAAM,EAAE;gBACvB,OAAO,EAAE,CAAA;aACV;YACD,MAAM,CAAC,GAAG,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;YAC5E,MAAM,CAAC,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YACvD,IAAI,MAAM,CAAA;YACV,IAAI,KAAK,EAAE;gBACT,MAAM,GAAG,IAAI,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;aAChC;iBAAM;gBACL,MAAM,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;aAC3C;YACD,MAAM,SAAS,GAAG,WAAW,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;YACnE,IAAI,CAAC,GAAG,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE;gBACpC,MAAM,IAAI,KAAK,CAAC,wCAAwC,CAAC,CAAA;aAC1D;YACD,IAAI,UAAU,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;YACjD,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE;gBAC9C,MAAM,CAAC,CAAC,CAAC,GAAG;oBACV,KAAK,EAAE,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,aAAa,GAAG,UAAU;oBACpD,KAAK,EAAE,CAAC,GAAG,CAAC;oBACZ,GAAG,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC;iBACf,CAAA;gBACD,UAAU,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;aAC9C;YACD,OAAO,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;gBACpB,uCAAY,CAAC,KAAE,KAAK,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,KAAK,CAAC,SAAS,CAAC,GAAG,SAAS,IAAE;YACjE,CAAC,CAAC,CAAA;QACJ,CAAC;KAAA;IAED;;;OAGG;IACH,QAAQ,CAAC,GAAW,EAAE,GAAW;QAC/B,GAAG,IAAI,CAAC,CAAA;QACR,OAAO;YACL,CAAC,CAAC,EAAE,CAAC,CAAC;YACN,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;YAClC,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;YAClC,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;YACpC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;YACtC,CAAC,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;SACzC,CAAA;IACH,CAAC;IAEK,cAAc,CAClB,KAAa,EACb,GAAW,EACX,GAAW,EACX,OAAiB,EAAE;;YAEnB,IAAI,GAAG,GAAG,CAAC,EAAE;gBACX,GAAG,GAAG,CAAC,CAAA;aACR;YAED,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,IAAI,CAAC,SAAS,EAAE;gBACd,OAAO,EAAE,CAAA;aACV;YACD,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YACnC,IAAI,CAAC,EAAE,EAAE;gBACP,OAAO,EAAE,CAAA;aACV;YAED,uCAAuC;YACvC,MAAM,eAAe,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;YAC/C,MAAM,MAAM,GAAY,EAAE,CAAA;YAE1B,sEAAsE;YACtE,KAAK,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,eAAe,EAAE;gBAC1C,KAAK,IAAI,GAAG,GAAG,KAAK,EAAE,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,EAAE;oBACvC,IAAI,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE;wBACpB,MAAM,SAAS,GAAG,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAA;wBAClC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;4BACzC,MAAM,CAAC,IAAI,CAAC,IAAI,eAAK,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAA;yBAClE;qBACF;iBACF;aACF;YAED,0EAA0E;YAC1E,mCAAmC;YACnC,MAAM,KAAK,GAAG,EAAE,CAAC,WAAW,CAAC,MAAM,CAAA;YACnC,IAAI,MAAM,GAAG,IAAI,CAAA;YACjB,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;YAC7C,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;YAC7C,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,IAAI,MAAM,EAAE,EAAE,CAAC,EAAE;gBACrC,MAAM,EAAE,GAAG,EAAE,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;gBAC5B,IAAI,EAAE,EAAE;oBACN,IAAI,CAAC,MAAM,IAAI,EAAE,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE;wBACvC,MAAM,GAAG,EAAE,CAAA;qBACZ;iBACF;aACF;YAED,OAAO,IAAA,qBAAc,EAAC,MAAM,EAAE,MAAM,CAAC,CAAA;QACvC,CAAC;KAAA;CACF;AAlND,sBAkNC"}
+{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":";;;;;;;;;;;;;;AAAA,mDAA0D;AAC1D,oDAA2B;AAE3B,iCAAgF;AAChF,4DAAmC;AAEnC,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEnC,SAAS,SAAS,CAAC,CAAS,EAAE,QAAgB;IAC5C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAA;AAC3B,CAAC;AACD,SAAS,OAAO,CAAC,CAAS,EAAE,QAAgB;IAC1C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,GAAG,QAAQ,CAAA;AACtC,CAAC;AAED,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,GAAG,IAAI,CAAC,CAAA;IACR,OAAO;QACL,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACpC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACtC,CAAC,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;KACzC,CAAA;AACH,CAAC;AAED,MAAqB,GAAI,SAAQ,mBAAS;IAGlC,SAAS,CAAC,KAAa,EAAE,IAAe;;;YAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,OAAO,CAAA,MAAA,MAAA,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,0CAAE,KAAK,0CAAE,SAAS,KAAI,CAAC,CAAA;;KACvD;IAED,4BAA4B;IACtB,MAAM,CAAC,IAAe;;YAC1B,MAAM,KAAK,GAAG,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAW,CAAA;YAE9D,0BAA0B;YAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE;gBACvC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;aAClC;YAED,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACrC,MAAM,KAAK,GAAG,CAAC,CAAA;YACf,MAAM,QAAQ,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;YAEnD,+CAA+C;YAC/C,IAAI,IAAI,GAAG,CAAC,CAAA;YACZ,IAAI,aAAwC,CAAA;YAI5C,MAAM,OAAO,GAAG,IAAI,KAAK,CAItB,QAAQ,CAAC,CAAA;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE;gBACjC,oBAAoB;gBACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;gBACxC,IAAI,KAAK,CAAA;gBAET,IAAI,IAAI,CAAC,CAAA;gBACT,MAAM,QAAQ,GAA+B,EAAE,CAAA;gBAE/C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;oBACpC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,IAAI,CAAC,CAAA;oBACpC,IAAI,IAAI,CAAC,CAAA;oBACT,IAAI,GAAG,KAAK,QAAQ,GAAG,CAAC,EAAE;wBACxB,IAAI,IAAI,CAAC,CAAA;wBACT,KAAK,GAAG,IAAA,qBAAc,EAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;wBACxC,IAAI,IAAI,EAAE,CAAA;qBACX;yBAAM,IAAI,GAAG,GAAG,QAAQ,GAAG,CAAC,EAAE;wBAC7B,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;qBACpE;yBAAM;wBACL,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;wBAC1C,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,MAAM,GAAG,IAAI,KAAK,CAAQ,UAAU,CAAC,CAAA;wBAC3C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE;4BACnC,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;4BAChC,IAAI,IAAI,CAAC,CAAA;4BACT,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;4BAChC,IAAI,IAAI,CAAC,CAAA;4BACT,aAAa,GAAG,IAAA,oBAAa,EAAC,aAAa,EAAE,CAAC,CAAC,CAAA;4BAC/C,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,eAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;yBACjC;wBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;qBACvB;iBACF;gBAED,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;gBAC3C,IAAI,IAAI,CAAC,CAAA;gBACT,mEAAmE;gBACnE,qEAAqE;gBACrE,OAAO;gBACP,MAAM,WAAW,GAAG,IAAI,KAAK,CAAgB,WAAW,CAAC,CAAA;gBACzD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE;oBACpC,MAAM,MAAM,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;oBACrC,IAAI,IAAI,CAAC,CAAA;oBACT,aAAa,GAAG,IAAA,oBAAa,EAAC,aAAa,EAAE,MAAM,CAAC,CAAA;oBACpD,WAAW,CAAC,CAAC,CAAC,GAAG,MAAM,CAAA;iBACxB;gBAED,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,CAAA;aAC9C;YAED,OAAO;gBACL,GAAG,EAAE,IAAI;gBACT,aAAa;gBACb,YAAY,EAAE,CAAC,IAAI,EAAE;gBACrB,OAAO;gBACP,QAAQ;aACT,CAAA;QACH,CAAC;KAAA;IAEK,QAAQ,CACZ,KAAa,EACb,KAAc,EACd,GAAY,EACZ,OAAiB,EAAE;;YAEnB,MAAM,CAAC,GAAG,KAAK,CAAA;YACf,MAAM,KAAK,GAAG,KAAK,KAAK,SAAS,CAAA;YACjC,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,MAAM,MAAM,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YACvC,IAAI,CAAC,MAAM,EAAE;gBACX,OAAO,EAAE,CAAA;aACV;YACD,MAAM,EAAE,WAAW,GAAG,EAAE,EAAE,KAAK,EAAE,GAAG,MAAM,CAAA;YAC1C,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE;gBAC5B,OAAO,EAAE,CAAA;aACV;YACD,MAAM,CAAC,GAAG,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC5E,MAAM,CAAC,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,EAAE,CAAC,CAAC,CAAA;YACvD,MAAM,MAAM,GAAG,KAAK;gBAClB,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC;gBACxB,CAAC,CAAC,IAAI,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;YACrC,MAAM,SAAS,GAAG,WAAW,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;YACnE,IAAI,CAAC,GAAG,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE;gBACpC,MAAM,IAAI,KAAK,CAAC,wCAAwC,CAAC,CAAA;aAC1D;YACD,IAAI,UAAU,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;YACjD,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE;gBAC9C,MAAM,CAAC,CAAC,CAAC,GAAG;oBACV,KAAK,EAAE,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,aAAa,GAAG,UAAU;oBACpD,KAAK,EAAE,CAAC,GAAG,CAAC;oBACZ,GAAG,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC;iBACf,CAAA;gBACD,UAAU,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;aAC9C;YACD,OAAO,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,iCAClB,CAAC,KACJ,KAAK,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAA,KAAK,aAAL,KAAK,uBAAL,KAAK,CAAE,SAAS,KAAI,CAAC,CAAC,CAAC,GAAG,SAAS,IACtD,CAAC,CAAA;QACL,CAAC;KAAA;IAEK,cAAc,CAClB,KAAa,EACb,GAAW,EACX,GAAW,EACX,OAAiB,EAAE;;YAEnB,IAAI,GAAG,GAAG,CAAC,EAAE;gBACX,GAAG,GAAG,CAAC,CAAA;aACR;YAED,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,IAAI,CAAC,SAAS,EAAE;gBACd,OAAO,EAAE,CAAA;aACV;YACD,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YACnC,IAAI,CAAC,EAAE,EAAE;gBACP,OAAO,EAAE,CAAA;aACV;YAED,uCAAuC;YACvC,MAAM,eAAe,GAAG,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;YAC1C,MAAM,MAAM,GAAY,EAAE,CAAA;YAE1B,sEAAsE;YACtE,KAAK,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,eAAe,EAAE;gBAC1C,KAAK,IAAI,GAAG,GAAG,KAAK,EAAE,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,EAAE;oBACvC,IAAI,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE;wBACpB,MAAM,SAAS,GAAG,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAA;wBAClC,KAAK,MAAM,QAAQ,IAAI,SAAS,EAAE;4BAChC,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;yBACtB;qBACF;iBACF;aACF;YAED,0EAA0E;YAC1E,mCAAmC;YACnC,MAAM,KAAK,GAAG,EAAE,CAAC,WAAW,CAAC,MAAM,CAAA;YACnC,IAAI,MAAiC,CAAA;YACrC,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;YAC7C,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;YAC7C,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,IAAI,MAAM,EAAE,EAAE,CAAC,EAAE;gBACrC,MAAM,EAAE,GAAG,EAAE,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;gBAC5B,IAAI,EAAE,IAAI,CAAC,CAAC,MAAM,IAAI,EAAE,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,EAAE;oBAC/C,MAAM,GAAG,EAAE,CAAA;iBACZ;aACF;YAED,OAAO,IAAA,qBAAc,EAAC,MAAM,EAAE,MAAM,CAAC,CAAA;QACvC,CAAC;KAAA;IAEK,KAAK,CAAC,OAAiB,EAAE;;YAC7B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;gBAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;oBACxC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;oBACvB,MAAM,CAAC,CAAA;gBACT,CAAC,CAAC,CAAA;aACH;YACD,OAAO,IAAI,CAAC,MAAM,CAAA;QACpB,CAAC;KAAA;IAEK,SAAS,CAAC,KAAa,EAAE,OAAiB,EAAE;;;YAChD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACrC,OAAO,CAAC,CAAC,CAAA,MAAA,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,0CAAE,QAAQ,CAAA,CAAA;;KACzC;CACF;AApMD,sBAoMC"}

package/dist/bamFile.d.ts

@@ -1,28 +1,27 @@
 /// <reference types="node" />
+import { Buffer } from 'buffer';
 import { GenericFilehandle } from 'generic-filehandle';
+import BAI from './bai';
+import CSI from './csi';
 import Chunk from './chunk';
 import BAMFeature from './record';
 import { BamOpts, BaseOpts } from './util';
 export declare const BAM_MAGIC = 21840194;
 export default class BamFile {
-    private renameRefSeq;
-    private bam;
-    private index;
-    private chunkSizeLimit;
-    private fetchSizeLimit;
-    private header;
-    protected chrToIndex: any;
-    protected indexToChr: any;
-    private yieldThreadTime;
+    renameRefSeq: (a: string) => string;
+    bam: GenericFilehandle;
+    header?: string;
+    chrToIndex?: Record<string, number>;
+    indexToChr?: {
+        refName: string;
+        length: number;
+    }[];
+    yieldThreadTime: number;
+    index?: BAI | CSI;
+    htsget: boolean;
+    headerP?: ReturnType<BamFile['getHeaderPre']>;
     private featureCache;
-    /**
-     * @param {object} args
-     * @param {string} [args.bamPath]
-     * @param {FileHandle} [args.bamFilehandle]
-     * @param {string} [args.baiPath]
-     * @param {FileHandle} [args.baiFilehandle]
-     */
-    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, fetchSizeLimit, chunkSizeLimit, yieldThreadTime, renameRefSeqs, }: {
+    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, yieldThreadTime, renameRefSeqs, }: {
         bamFilehandle?: GenericFilehandle;
         bamPath?: string;
         bamUrl?: string;
@@ -32,19 +31,25 @@ export default class BamFile {
         csiPath?: string;
         csiFilehandle?: GenericFilehandle;
         csiUrl?: string;
-        fetchSizeLimit?: number;
-        chunkSizeLimit?: number;
         renameRefSeqs?: (a: string) => string;
         yieldThreadTime?: number;
+        htsget?: boolean;
     });
-    getHeader(origOpts?: AbortSignal | BaseOpts): Promise<{
+    getHeaderPre(origOpts?: BaseOpts): Promise<{
         tag: string;
         data: {
             tag: string;
             value: string;
         }[];
-    }[]>;
-    getHeaderText(opts?: BaseOpts): Promise<any>;
+    }[] | undefined>;
+    getHeader(opts?: BaseOpts): Promise<{
+        tag: string;
+        data: {
+            tag: string;
+            value: string;
+        }[];
+    }[] | undefined>;
+    getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
     _readRefSeqs(start: number, refSeqBytes: number, opts?: BaseOpts): Promise<{
         chrToIndex: {
             [key: string]: number;
@@ -56,19 +61,20 @@ export default class BamFile {
     }>;
     getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<BAMFeature[]>;
     streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
-    _fetchChunkFeatures(chunks: Chunk[], chrId: number, min: number, max: number, opts: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
+    _fetchChunkFeatures(chunks: Chunk[], chrId: number, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
     fetchPairs(chrId: number, feats: BAMFeature[][], opts: BamOpts): Promise<BAMFeature[]>;
+    _readRegion(position: number, size: number, opts?: BaseOpts): Promise<Buffer>;
     _readChunk({ chunk, opts }: {
         chunk: Chunk;
         opts: BaseOpts;
     }): Promise<{
-        data: any;
-        cpositions: any;
-        dpositions: any;
+        data: Buffer;
+        cpositions: number[];
+        dpositions: number[];
         chunk: Chunk;
     }>;
     readBamFeatures(ba: Buffer, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<BAMFeature[]>;
-    hasRefSeq(seqName: string): Promise<boolean>;
+    hasRefSeq(seqName: string): Promise<boolean | undefined>;
     lineCount(seqName: string): Promise<number>;
     indexCov(seqName: string, start?: number, end?: number): Promise<{
         start: number;