@gmod/bam 5.0.6 → 6.0.0

package/esm/record.js

@@ -1,26 +1,36 @@
-import Constants from './constants';
+var __classPrivateFieldSet = (this && this.__classPrivateFieldSet) || function (receiver, state, value, kind, f) {
+    if (kind === "m") throw new TypeError("Private method is not writable");
+    if (kind === "a" && !f) throw new TypeError("Private accessor was defined without a setter");
+    if (typeof state === "function" ? receiver !== state || !f : !state.has(receiver)) throw new TypeError("Cannot write private member to an object whose class did not declare it");
+    return (kind === "a" ? f.call(receiver, value) : f ? f.value = value : state.set(receiver, value)), value;
+};
+var __classPrivateFieldGet = (this && this.__classPrivateFieldGet) || function (receiver, state, kind, f) {
+    if (kind === "a" && !f) throw new TypeError("Private accessor was defined without a getter");
+    if (typeof state === "function" ? receiver !== state || !f : !state.has(receiver)) throw new TypeError("Cannot read private member from an object whose class did not declare it");
+    return kind === "m" ? f : kind === "a" ? f.call(receiver) : f ? f.value : state.get(receiver);
+};
+var _BamRecord_dataView;
+import Constants from "./constants.js";
 const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('');
 const CIGAR_DECODER = 'MIDNSHP=X???????'.split('');
-export default class BamRecord {
-    fileOffset;
-    bytes;
-    #dataView;
+class BamRecord {
     constructor(args) {
+        _BamRecord_dataView.set(this, void 0);
         this.bytes = args.bytes;
         this.fileOffset = args.fileOffset;
-        this.#dataView = new DataView(this.bytes.byteArray.buffer);
+        __classPrivateFieldSet(this, _BamRecord_dataView, new DataView(this.bytes.byteArray.buffer), "f");
     }
     get byteArray() {
         return this.bytes.byteArray;
     }
     get flags() {
-        return ((this.#dataView.getInt32(this.bytes.start + 16, true) & 0xffff0000) >> 16);
+        return ((__classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(this.bytes.start + 16, true) & 0xffff0000) >> 16);
     }
     get ref_id() {
-        return this.#dataView.getInt32(this.bytes.start + 4, true);
+        return __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(this.bytes.start + 4, true);
     }
     get start() {
-        return this.#dataView.getInt32(this.bytes.start + 8, true);
+        return __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(this.bytes.start + 8, true);
     }
     get end() {
         return this.start + this.length_on_ref;
@@ -75,31 +85,31 @@ export default class BamRecord {
                 p += 1;
             }
             else if (type === 'i') {
-                tags[tag] = this.#dataView.getInt32(p, true);
+                tags[tag] = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(p, true);
                 p += 4;
             }
             else if (type === 'I') {
-                tags[tag] = this.#dataView.getUint32(p, true);
+                tags[tag] = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getUint32(p, true);
                 p += 4;
             }
             else if (type === 'c') {
-                tags[tag] = this.#dataView.getInt8(p);
+                tags[tag] = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt8(p);
                 p += 1;
             }
             else if (type === 'C') {
-                tags[tag] = this.#dataView.getUint8(p);
+                tags[tag] = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getUint8(p);
                 p += 1;
             }
             else if (type === 's') {
-                tags[tag] = this.#dataView.getInt16(p, true);
+                tags[tag] = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt16(p, true);
                 p += 2;
             }
             else if (type === 'S') {
-                tags[tag] = this.#dataView.getUint16(p, true);
+                tags[tag] = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getUint16(p, true);
                 p += 2;
             }
             else if (type === 'f') {
-                tags[tag] = this.#dataView.getFloat32(p, true);
+                tags[tag] = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getFloat32(p, true);
                 p += 4;
             }
             else if (type === 'Z' || type === 'H') {
@@ -118,13 +128,13 @@ export default class BamRecord {
             else if (type === 'B') {
                 const cc = this.byteArray[p++];
                 const Btype = String.fromCharCode(cc);
-                const limit = this.#dataView.getInt32(p, true);
+                const limit = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(p, true);
                 p += 4;
                 if (Btype === 'i') {
                     if (tag === 'CG') {
                         const value = [];
                         for (let k = 0; k < limit; k++) {
-                            const cigop = this.#dataView.getInt32(p, true);
+                            const cigop = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(p, true);
                             const lop = cigop >> 4;
                             const op = CIGAR_DECODER[cigop & 0xf];
                             value.push(lop + op);
@@ -135,7 +145,7 @@ export default class BamRecord {
                     else {
                         const value = [];
                         for (let k = 0; k < limit; k++) {
-                            value.push(this.#dataView.getInt32(p, true));
+                            value.push(__classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(p, true));
                             p += 4;
                         }
                         tags[tag] = value;
@@ -145,7 +155,7 @@ export default class BamRecord {
                     if (tag === 'CG') {
                         const value = [];
                         for (let k = 0; k < limit; k++) {
-                            const cigop = this.#dataView.getUint32(p, true);
+                            const cigop = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getUint32(p, true);
                             const lop = cigop >> 4;
                             const op = CIGAR_DECODER[cigop & 0xf];
                             value.push(lop + op);
@@ -156,7 +166,7 @@ export default class BamRecord {
                     else {
                         const value = [];
                         for (let k = 0; k < limit; k++) {
-                            value.push(this.#dataView.getUint32(p, true));
+                            value.push(__classPrivateFieldGet(this, _BamRecord_dataView, "f").getUint32(p, true));
                             p += 4;
                         }
                         tags[tag] = value;
@@ -165,7 +175,7 @@ export default class BamRecord {
                 else if (Btype === 's') {
                     const value = [];
                     for (let k = 0; k < limit; k++) {
-                        value.push(this.#dataView.getInt16(p, true));
+                        value.push(__classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt16(p, true));
                         p += 2;
                     }
                     tags[tag] = value;
@@ -173,7 +183,7 @@ export default class BamRecord {
                 else if (Btype === 'S') {
                     const value = [];
                     for (let k = 0; k < limit; k++) {
-                        value.push(this.#dataView.getUint16(p, true));
+                        value.push(__classPrivateFieldGet(this, _BamRecord_dataView, "f").getUint16(p, true));
                         p += 2;
                     }
                     tags[tag] = value;
@@ -181,7 +191,7 @@ export default class BamRecord {
                 else if (Btype === 'c') {
                     const value = [];
                     for (let k = 0; k < limit; k++) {
-                        value.push(this.#dataView.getInt8(p));
+                        value.push(__classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt8(p));
                         p += 1;
                     }
                     tags[tag] = value;
@@ -189,7 +199,7 @@ export default class BamRecord {
                 else if (Btype === 'C') {
                     const value = [];
                     for (let k = 0; k < limit; k++) {
-                        value.push(this.#dataView.getUint8(p));
+                        value.push(__classPrivateFieldGet(this, _BamRecord_dataView, "f").getUint8(p));
                         p += 1;
                     }
                     tags[tag] = value;
@@ -197,7 +207,7 @@ export default class BamRecord {
                 else if (Btype === 'f') {
                     const value = [];
                     for (let k = 0; k < limit; k++) {
-                        value.push(this.#dataView.getFloat32(p, true));
+                        value.push(__classPrivateFieldGet(this, _BamRecord_dataView, "f").getFloat32(p, true));
                         p += 4;
                     }
                     tags[tag] = value;
@@ -273,14 +283,14 @@ export default class BamRecord {
         const CIGAR = [];
         // check for CG tag by inspecting whether the CIGAR field contains a clip
         // that consumes entire seqLen
-        let cigop = this.#dataView.getInt32(p, true);
+        let cigop = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(p, true);
         let lop = cigop >> 4;
         let op = CIGAR_DECODER[cigop & 0xf];
         if (op === 'S' && lop === this.seq_length) {
             // if there is a CG the second CIGAR field will be a N tag the represents
             // the length on ref
             p += 4;
-            cigop = this.#dataView.getInt32(p, true);
+            cigop = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(p, true);
             lop = cigop >> 4;
             op = CIGAR_DECODER[cigop & 0xf];
             if (op !== 'N') {
@@ -294,7 +304,7 @@ export default class BamRecord {
         else {
             let lref = 0;
             for (let c = 0; c < numCigarOps; ++c) {
-                cigop = this.#dataView.getInt32(p, true);
+                cigop = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(p, true);
                 lop = cigop >> 4;
                 op = CIGAR_DECODER[cigop & 0xf];
                 CIGAR.push(lop + op);
@@ -379,22 +389,22 @@ export default class BamRecord {
         return undefined;
     }
     get bin_mq_nl() {
-        return this.#dataView.getInt32(this.bytes.start + 12, true);
+        return __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(this.bytes.start + 12, true);
     }
     get flag_nc() {
-        return this.#dataView.getInt32(this.bytes.start + 16, true);
+        return __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(this.bytes.start + 16, true);
     }
     get seq_length() {
-        return this.#dataView.getInt32(this.bytes.start + 20, true);
+        return __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(this.bytes.start + 20, true);
     }
     get next_refid() {
-        return this.#dataView.getInt32(this.bytes.start + 24, true);
+        return __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(this.bytes.start + 24, true);
     }
     get next_pos() {
-        return this.#dataView.getInt32(this.bytes.start + 28, true);
+        return __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(this.bytes.start + 28, true);
     }
     get template_length() {
-        return this.#dataView.getInt32(this.bytes.start + 32, true);
+        return __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(this.bytes.start + 32, true);
     }
     toJSON() {
         const data = {};
@@ -408,6 +418,8 @@ export default class BamRecord {
         return data;
     }
 }
+_BamRecord_dataView = new WeakMap();
+export default BamRecord;
 function cacheGetter(ctor, prop) {
     const desc = Object.getOwnPropertyDescriptor(ctor.prototype, prop);
     if (!desc) {

package/esm/record.js.map

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package/esm/util.d.ts

@@ -1,5 +1,5 @@
-import Chunk from './chunk';
-import { Offset, VirtualOffset } from './virtualOffset';
+import Chunk from './chunk.ts';
+import { Offset, VirtualOffset } from './virtualOffset.ts';
 export declare function timeout(ms: number): Promise<unknown>;
 /**
  * Properly check if the given AbortSignal is aborted.

package/esm/util.js

@@ -1,4 +1,4 @@
-import { longFromBytesToUnsigned } from './long';
+import { longFromBytesToUnsigned } from "./long.js";
 export function timeout(ms) {
     return new Promise(resolve => setTimeout(resolve, ms));
 }

package/esm/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,uBAAuB,EAAE,MAAM,WAAW,CAAA;AAGnD,MAAM,UAAU,OAAO,CAAC,EAAU;IAChC,OAAO,IAAI,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAA;AACxD,CAAC;AAED;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAM;IACR,CAAC;IAED,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;QACnB,8BAA8B;QAC9B,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE,CAAC;YACxC,MAAM,CAAC,GAAG,IAAI,KAAK,CAAC,SAAS,CAAC,CAAA;YAC9B,aAAa;YACb,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;QACT,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;QACjD,CAAC;IACH,CAAC;AACH,CAAC;AAED;;;;;GAKG;AACH,MAAM,CAAC,KAAK,UAAU,eAAe,CAAC,MAAoB;IACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;IACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;AAC1B,CAAC;AAED,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,YAAY,GAAY,EAAE,CAAA;IAChC,IAAI,SAA4B,CAAA;IAEhC,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACxB,OAAO,MAAM,CAAA;IACf,CAAC;IAED,MAAM,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE;QACrB,MAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC,GAAG,CAAA;IACtE,CAAC,CAAC,CAAA;IAEF,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;QAC3B,IAAI,CAAC,MAAM,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;YAChD,IAAI,SAAS,KAAK,SAAS,EAAE,CAAC;gBAC5B,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;gBACxB,SAAS,GAAG,KAAK,CAAA;YACnB,CAAC;iBAAM,CAAC;gBACN,IAAI,cAAc,CAAC,SAAS,EAAE,KAAK,CAAC,EAAE,CAAC;oBACrC,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;wBAC7C,SAAS,CAAC,IAAI,GAAG,KAAK,CAAC,IAAI,CAAA;oBAC7B,CAAC;gBACH,CAAC;qBAAM,CAAC;oBACN,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;oBACxB,SAAS,GAAG,KAAK,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,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,GAAG,CAAC,KAAmB;IACrC,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,KAAK,MAAM,KAAK,IAAI,KAAK,EAAE,CAAC;QAC1B,GAAG,IAAI,KAAK,CAAC,MAAM,CAAA;IACrB,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AACD,MAAM,UAAU,gBAAgB,CAAC,IAAkB;IACjD,MAAM,WAAW,GAAG,IAAI,UAAU,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAA;IAC7C,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,IAAI,GAAG,GAAQ,EAAE,CAAA;IACjB,IAAI,KAAK,EAAE,MAAM,CAAC,IAAI,GAAG,EAAE,CAAC;QAC1B,GAAG,GAAG,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAA;IACrB,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}

package/esm/virtualOffset.js

@@ -1,6 +1,4 @@
 export class VirtualOffset {
-    blockPosition;
-    dataPosition;
     constructor(blockPosition, dataPosition) {
         this.blockPosition = blockPosition; // < offset of the compressed data block
         this.dataPosition = dataPosition; // < offset into the uncompressed data

package/esm/virtualOffset.js.map

@@ -1 +1 @@
-{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":"AAOA,MAAM,OAAO,aAAa;IACjB,aAAa,CAAQ;IACrB,YAAY,CAAQ;IAC3B,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;CACF;AACD,MAAM,UAAU,SAAS,CAAC,KAAiB,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACxE,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;IACpE,CAAC;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,aAAa;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,WAAW;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,SAAS;QAC9B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,OAAO;QAC5B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,KAAK;QAC1B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,EACpB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAE,CAC3C,CAAA;AACH,CAAC"}
+{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":"AAOA,MAAM,OAAO,aAAa;IAGxB,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;CACF;AACD,MAAM,UAAU,SAAS,CAAC,KAAiB,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACxE,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;IACpE,CAAC;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,aAAa;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,WAAW;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,SAAS;QAC9B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,OAAO;QAC5B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,KAAK;QAC1B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,EACpB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAE,CAC3C,CAAA;AACH,CAAC"}

package/package.json

@@ -1,11 +1,19 @@
 {
   "name": "@gmod/bam",
-  "version": "5.0.6",
+  "version": "6.0.0",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": "GMOD/bam-js",
-  "main": "dist/index.js",
-  "module": "esm/index.js",
+  "type": "module",
+  "types": "./dist/index.d.ts",
+  "exports": {
+    "import": {
+      "import": "./esm/index.js"
+    },
+    "require": {
+      "require": "./dist/index.js"
+    }
+  },
   "author": {
     "name": "Colin Diesh",
     "email": "colin.diesh@gmail.com",
@@ -41,23 +49,21 @@
     "@gmod/abortable-promise-cache": "^2.0.0",
     "@gmod/bgzf-filehandle": "^2.0.1",
     "crc": "^4.3.2",
-    "generic-filehandle2": "^1.0.0",
+    "generic-filehandle2": "^2.0.1",
     "quick-lru": "^4.0.0"
   },
   "devDependencies": {
-    "@types/node": "^20.11.19",
-    "@typescript-eslint/eslint-plugin": "^8.1.0",
-    "@typescript-eslint/parser": "^8.1.0",
-    "@vitest/coverage-v8": "^3.0.1",
+    "@types/node": "^22.15.3",
+    "@vitest/coverage-v8": "^3.0.9",
     "eslint": "^9.9.0",
     "eslint-plugin-import": "^2.31.0",
-    "eslint-plugin-unicorn": "^56.0.0",
+    "eslint-plugin-unicorn": "^59.0.0",
     "prettier": "^3.3.3",
     "rimraf": "^6.0.1",
     "standard-changelog": "^6.0.0",
     "typescript": "^5.0.4",
-    "typescript-eslint": "^8.1.0",
-    "vitest": "^3.0.1"
+    "typescript-eslint": "^8.27.0",
+    "vitest": "^3.0.9"
   },
   "publishConfig": {
     "access": "public"

package/src/bai.ts

@@ -1,9 +1,14 @@
 import QuickLRU from 'quick-lru'
 
-import Chunk from './chunk'
-import IndexFile from './indexFile'
-import { BaseOpts, findFirstData, optimizeChunks, parsePseudoBin } from './util'
-import { VirtualOffset, fromBytes } from './virtualOffset'
+import Chunk from './chunk.ts'
+import IndexFile from './indexFile.ts'
+import {
+  BaseOpts,
+  findFirstData,
+  optimizeChunks,
+  parsePseudoBin,
+} from './util.ts'
+import { VirtualOffset, fromBytes } from './virtualOffset.ts'
 
 const BAI_MAGIC = 21578050 // BAI\1
 

package/src/bamFile.ts

@@ -1,33 +1,21 @@
-import AbortablePromiseCache from '@gmod/abortable-promise-cache'
 import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle'
 import crc32 from 'crc/calculators/crc32'
 import { LocalFile, RemoteFile } from 'generic-filehandle2'
-import QuickLRU from 'quick-lru'
-
-import BAI from './bai'
-import Chunk from './chunk'
-import CSI from './csi'
-import NullFilehandle from './nullFilehandle'
-import BAMFeature from './record'
-import { parseHeaderText } from './sam'
-import {
-  BamOpts,
-  BaseOpts,
-  checkAbortSignal,
-  gen2array,
-  makeOpts,
-  timeout,
-} from './util'
 
+import BAI from './bai.ts'
+import Chunk from './chunk.ts'
+import CSI from './csi.ts'
+import NullFilehandle from './nullFilehandle.ts'
+import BAMFeature from './record.ts'
+import { parseHeaderText } from './sam.ts'
+import { checkAbortSignal, gen2array, makeOpts, timeout } from './util.ts'
+
+import type { BamOpts, BaseOpts } from './util.ts'
 import type { GenericFilehandle } from 'generic-filehandle2'
 
 export const BAM_MAGIC = 21840194
 
 const blockLen = 1 << 16
-interface Args {
-  chunk: Chunk
-  opts: BaseOpts
-}
 
 export default class BamFile {
   public renameRefSeq: (a: string) => string
@@ -40,20 +28,6 @@ export default class BamFile {
   public htsget = false
   public headerP?: ReturnType<BamFile['getHeaderPre']>
 
-  private featureCache = new AbortablePromiseCache<Args, BAMFeature[]>({
-    cache: new QuickLRU({
-      maxSize: 50,
-    }),
-    fill: async (args: Args, signal) => {
-      const { chunk, opts } = args
-      const { data, cpositions, dpositions } = await this._readChunk({
-        chunk,
-        opts: { ...opts, signal },
-      })
-      return this.readBamFeatures(data, cpositions, dpositions, chunk)
-    },
-  })
-
   constructor({
     bamFilehandle,
     bamPath,
@@ -252,10 +226,15 @@ export default class BamFile {
     let done = false
 
     for (const chunk of chunks) {
-      const records = await this.featureCache.get(
-        chunk.toString(),
-        { chunk, opts },
-        opts.signal,
+      const { data, cpositions, dpositions } = await this._readChunk({
+        chunk,
+        opts,
+      })
+      const records = await this.readBamFeatures(
+        data,
+        cpositions,
+        dpositions,
+        chunk,
       )
 
       const recs = [] as BAMFeature[]

package/src/chunk.ts

@@ -1,4 +1,4 @@
-import { Offset } from './virtualOffset'
+import { Offset } from './virtualOffset.ts'
 
 // little class representing a chunk in the index
 export default class Chunk {

package/src/csi.ts

@@ -1,16 +1,17 @@
 import { unzip } from '@gmod/bgzf-filehandle'
 import QuickLRU from 'quick-lru'
 
-import Chunk from './chunk'
-import IndexFile from './indexFile'
+import Chunk from './chunk.ts'
+import IndexFile from './indexFile.ts'
 import {
-  BaseOpts,
   findFirstData,
   optimizeChunks,
   parseNameBytes,
   parsePseudoBin,
-} from './util'
-import { VirtualOffset, fromBytes } from './virtualOffset'
+} from './util.ts'
+import { VirtualOffset, fromBytes } from './virtualOffset.ts'
+
+import type { BaseOpts } from './util.ts'
 
 const CSI1_MAGIC = 21582659 // CSI\1
 const CSI2_MAGIC = 38359875 // CSI\2
@@ -118,8 +119,10 @@ export default class CSI extends IndexFile {
           const chunkCount = dataView.getInt32(curr, true)
           curr += 4
           for (let k = 0; k < chunkCount; k += 1) {
+            const u = fromBytes(bytes, curr)
             curr += 8
             curr += 8
+            firstDataLine = findFirstData(firstDataLine, u)
           }
         }
       }
@@ -138,12 +141,12 @@ export default class CSI extends IndexFile {
       const binCount = dataView.getInt32(curr, true)
       curr += 4
       const binIndex: Record<string, Chunk[]> = {}
-      let stats // < provided by parsing a pseudo-bin, if present
+      let pseudoBinStats
       for (let j = 0; j < binCount; j++) {
         const bin = dataView.getUint32(curr, true)
         curr += 4
         if (bin > maxBinNumber) {
-          stats = parsePseudoBin(bytes, curr + 28)
+          pseudoBinStats = parsePseudoBin(bytes, curr + 28)
           curr += 28 + 16
         } else {
           firstDataLine = findFirstData(firstDataLine, fromBytes(bytes, curr))
@@ -156,7 +159,6 @@ export default class CSI extends IndexFile {
             curr += 8
             const v = fromBytes(bytes, curr)
             curr += 8
-            firstDataLine = findFirstData(firstDataLine, u)
             chunks[k] = new Chunk(u, v, bin)
           }
           binIndex[bin] = chunks
@@ -165,7 +167,7 @@ export default class CSI extends IndexFile {
 
       return {
         binIndex,
-        stats,
+        stats: pseudoBinStats,
       }
     }
 

package/src/htsget.ts

@@ -1,14 +1,17 @@
 import { unzip } from '@gmod/bgzf-filehandle'
 
-import BamFile, { BAM_MAGIC } from './bamFile'
-import Chunk from './chunk'
-import { parseHeaderText } from './sam'
-import { BamOpts, BaseOpts, concatUint8Array } from './util'
+import BamFile, { BAM_MAGIC } from './bamFile.ts'
+import Chunk from './chunk.ts'
+import { parseHeaderText } from './sam.ts'
+import { concatUint8Array } from './util.ts'
+
+import type { BamOpts, BaseOpts } from './util.ts'
 
 interface HtsgetChunk {
   url: string
   headers?: Record<string, string>
 }
+
 async function concat(arr: HtsgetChunk[], opts?: Record<string, any>) {
   const res = await Promise.all(
     arr.map(async chunk => {

package/src/index.ts

@@ -1,5 +1,5 @@
-export { default as BAI } from './bai'
-export { default as BamFile } from './bamFile'
-export { default as CSI } from './csi'
-export { default as BamRecord } from './record'
-export { default as HtsgetFile } from './htsget'
+export { default as BAI } from './bai.ts'
+export { default as BamFile } from './bamFile.ts'
+export { default as CSI } from './csi.ts'
+export { default as BamRecord } from './record.ts'
+export { default as HtsgetFile } from './htsget.ts'

package/src/indexFile.ts

@@ -1,5 +1,5 @@
-import Chunk from './chunk'
-import { BaseOpts } from './util'
+import Chunk from './chunk.ts'
+import { BaseOpts } from './util.ts'
 
 import type { GenericFilehandle } from 'generic-filehandle2'
 
@@ -7,10 +7,6 @@ export default abstract class IndexFile {
   public filehandle: GenericFilehandle
   public renameRefSeq: (s: string) => string
 
-  /**
-   * @param {filehandle} filehandle
-   * @param {function} renameRefSeqs
-   */
   constructor({
     filehandle,
     renameRefSeq = (n: string) => n,

package/src/nullIndex.ts

@@ -1,4 +1,4 @@
-import IndexFile from './indexFile'
+import IndexFile from './indexFile.ts'
 
 export default class NullIndex extends IndexFile {
   public lineCount(): Promise<any> {