@gmod/bam 1.1.18 → 2.0.1

package/esm/record.d.ts

@@ -17,7 +17,7 @@ export default class BamRecord {
     seq_id(): number;
     _get(field: string): any;
     _tags(): string[];
-    parent(): undefined;
+    parent(): void;
     children(): any;
     id(): number;
     /**
@@ -75,7 +75,7 @@ export default class BamRecord {
     _seq_bytes(): number;
     getReadBases(): string;
     seq(): string;
-    getPairOrientation(): string | null;
+    getPairOrientation(): string;
     _bin_mq_nl(): number;
     _flag_nc(): number;
     seq_length(): number;

package/esm/record.js

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/no-empty-function */
 import Constants from './constants';
 const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('');
 const CIGAR_DECODER = 'MIDNSHP=X???????'.split('');
@@ -57,11 +56,11 @@ export default class BamRecord {
             tags.push('next_segment_position', 'pair_orientation');
         }
         tags = tags.concat(this._tagList || []);
-        Object.keys(this.data).forEach(k => {
+        for (const k of Object.keys(this.data)) {
             if (k[0] !== '_' && k !== 'next_seq_id') {
                 tags.push(k);
             }
-        });
+        }
         const seen = {};
         return tags.filter(t => {
             if ((t in this.data && this.data[t] === undefined) ||
@@ -76,7 +75,7 @@ export default class BamRecord {
         });
     }
     parent() {
-        return undefined;
+        return;
     }
     children() {
         return this.get('subfeatures');
@@ -101,7 +100,7 @@ export default class BamRecord {
     }
     qualRaw() {
         if (this.isSegmentUnmapped()) {
-            return undefined;
+            return;
         }
         const { start, byteArray } = this.bytes;
         const p = start +
@@ -117,7 +116,7 @@ export default class BamRecord {
     }
     multi_segment_next_segment_strand() {
         if (this.isMateUnmapped()) {
-            return undefined;
+            return;
         }
         return this.isMateReverseComplemented() ? -1 : 1;
     }
@@ -138,7 +137,7 @@ export default class BamRecord {
         // called, we already know that we have no such tag, because
         // it would already have been cached.
         if (this._allTagsParsed) {
-            return undefined;
+            return;
         }
         const { byteArray, start } = this.bytes;
         let p = this._tagOffset ||
@@ -157,40 +156,48 @@ export default class BamRecord {
             p += 3;
             let value;
             switch (type) {
-                case 'A':
+                case 'A': {
                     value = String.fromCharCode(byteArray[p]);
                     p += 1;
                     break;
-                case 'i':
+                }
+                case 'i': {
                     value = byteArray.readInt32LE(p);
                     p += 4;
                     break;
-                case 'I':
+                }
+                case 'I': {
                     value = byteArray.readUInt32LE(p);
                     p += 4;
                     break;
-                case 'c':
+                }
+                case 'c': {
                     value = byteArray.readInt8(p);
                     p += 1;
                     break;
-                case 'C':
+                }
+                case 'C': {
                     value = byteArray.readUInt8(p);
                     p += 1;
                     break;
-                case 's':
+                }
+                case 's': {
                     value = byteArray.readInt16LE(p);
                     p += 2;
                     break;
-                case 'S':
+                }
+                case 'S': {
                     value = byteArray.readUInt16LE(p);
                     p += 2;
                     break;
-                case 'f':
+                }
+                case 'f': {
                     value = byteArray.readFloatLE(p);
                     p += 4;
                     break;
+                }
                 case 'Z':
-                case 'H':
+                case 'H': {
                     value = '';
                     while (p <= blockEnd) {
                         const cc = byteArray[p++];
@@ -202,6 +209,7 @@ export default class BamRecord {
                         }
                     }
                     break;
+                }
                 case 'B': {
                     value = '';
                     const cc = byteArray[p++];
@@ -295,10 +303,11 @@ export default class BamRecord {
                     }
                     break;
                 }
-                default:
+                default: {
                     console.warn(`Unknown BAM tag type '${type}', tags may be incomplete`);
                     value = undefined;
-                    p = blockEnd; // stop parsing tags
+                    p = blockEnd;
+                } // stop parsing tags
             }
             this._tagOffset = p;
             this._tagList.push(tag);
@@ -308,7 +317,7 @@ export default class BamRecord {
             this.data[lcTag] = value;
         }
         this._allTagsParsed = true;
-        return undefined;
+        return;
     }
     _parseAllTags() {
         this._parseTag('');
@@ -319,7 +328,7 @@ export default class BamRecord {
         cigar
             .match(/\d+\D/g)
             //@ts-ignore
-            .map(op => [op.match(/\D/)[0].toUpperCase(), parseInt(op, 10)]));
+            .map(op => [op.match(/\D/)[0].toUpperCase(), Number.parseInt(op, 10)]));
     }
     /**
      * @returns {boolean} true if the read is paired, regardless of whether both segments are mapped
@@ -373,7 +382,7 @@ export default class BamRecord {
     }
     cigar() {
         if (this.isSegmentUnmapped()) {
-            return undefined;
+            return;
         }
         const { byteArray, start } = this.bytes;
         const numCigarOps = this.get('_n_cigar_op');
@@ -492,7 +501,7 @@ export default class BamRecord {
             }
             return tmp.join('');
         }
-        return null;
+        return '';
     }
     _bin_mq_nl() {
         return this.bytes.byteArray.readInt32LE(this.bytes.start + 12);
@@ -514,13 +523,13 @@ export default class BamRecord {
     }
     toJSON() {
         const data = {};
-        Object.keys(this).forEach(k => {
+        for (const k of Object.keys(this)) {
             if (k.charAt(0) === '_' || k === 'bytes') {
-                return;
+                continue;
             }
             //@ts-ignore
             data[k] = this[k];
-        });
+        }
         return data;
     }
 }

package/esm/record.js.map

@@ -1 +1 @@
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package/esm/sam.js

@@ -1,16 +1,20 @@
 export function parseHeaderText(text) {
     const lines = text.split(/\r?\n/);
     const data = [];
-    lines.forEach(line => {
+    for (const line of lines) {
         const [tag, ...fields] = line.split(/\t/);
-        const parsedFields = fields.map(f => {
-            const [fieldTag, value] = f.split(':', 2);
-            return { tag: fieldTag, value };
-        });
         if (tag) {
-            data.push({ tag: tag.substr(1), data: parsedFields });
+            data.push({
+                tag: tag.slice(1),
+                data: fields.map(f => {
+                    const r = f.indexOf(':');
+                    const fieldTag = f.slice(0, r);
+                    const value = f.slice(r + 1);
+                    return { tag: fieldTag, value };
+                }),
+            });
         }
-    });
+    }
     return data;
 }
 //# sourceMappingURL=sam.js.map

package/esm/sam.js.map

@@ -1 +1 @@
-{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAA8D,EAAE,CAAA;IAC1E,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;QACnB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,MAAM,YAAY,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;YAClC,MAAM,CAAC,QAAQ,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YACzC,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;QACjC,CAAC,CAAC,CAAA;QACF,IAAI,GAAG,EAAE;YACP,IAAI,CAAC,IAAI,CAAC,EAAE,GAAG,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,CAAA;SACtD;IACH,CAAC,CAAC,CAAA;IACF,OAAO,IAAI,CAAA;AACb,CAAC"}
+{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAA8D,EAAE,CAAA;IAC1E,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,IAAI,GAAG,EAAE,CAAC;YACR,IAAI,CAAC,IAAI,CAAC;gBACR,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;gBACjB,IAAI,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;oBACnB,MAAM,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;oBACxB,MAAM,QAAQ,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;oBAC9B,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;oBAC5B,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;gBACjC,CAAC,CAAC;aACH,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}

package/esm/util.d.ts

@@ -1,3 +1,5 @@
+/// <reference types="node" />
+import Long from 'long';
 import Chunk from './chunk';
 import VirtualOffset from './virtualOffset';
 export declare function timeout(ms: number): Promise<unknown>;
@@ -32,4 +34,14 @@ export interface BaseOpts {
     signal?: AbortSignal;
 }
 export declare function makeOpts(obj?: AbortSignal | BaseOpts): BaseOpts;
-export declare function optimizeChunks(chunks: Chunk[], lowest: VirtualOffset): Chunk[];
+export declare function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset): Chunk[];
+export declare function parsePseudoBin(bytes: Buffer, offset: number): {
+    lineCount: number;
+};
+export declare function findFirstData(firstDataLine: VirtualOffset | undefined, virtualOffset: VirtualOffset): VirtualOffset;
+export declare function parseNameBytes(namesBytes: Buffer, renameRefSeq?: (arg: string) => string): {
+    refNameToId: {
+        [key: string]: number;
+    };
+    refIdToName: string[];
+};

package/esm/util.js

@@ -1,3 +1,4 @@
+import Long from 'long';
 export function timeout(ms) {
     return new Promise(resolve => setTimeout(resolve, ms));
 }
@@ -25,15 +26,15 @@ export function checkAbortSignal(signal) {
     }
     if (signal.aborted) {
         // console.log('bam aborted!')
-        if (typeof DOMException !== 'undefined') {
-            throw new DOMException('aborted', 'AbortError');
-        }
-        else {
+        if (typeof DOMException === 'undefined') {
             const e = new Error('aborted');
             //@ts-ignore
             e.code = 'ERR_ABORTED';
             throw e;
         }
+        else {
+            throw new DOMException('aborted', 'AbortError');
+        }
     }
 }
 /**
@@ -55,22 +56,17 @@ export function makeOpts(obj = {}) {
 }
 export function optimizeChunks(chunks, lowest) {
     const mergedChunks = [];
-    let lastChunk = null;
+    let lastChunk;
     if (chunks.length === 0) {
         return chunks;
     }
     chunks.sort((c0, c1) => {
         const dif = c0.minv.blockPosition - c1.minv.blockPosition;
-        if (dif !== 0) {
-            return dif;
-        }
-        else {
-            return c0.minv.dataPosition - c1.minv.dataPosition;
-        }
+        return dif === 0 ? c0.minv.dataPosition - c1.minv.dataPosition : dif;
     });
-    chunks.forEach(chunk => {
+    for (const chunk of chunks) {
         if (!lowest || chunk.maxv.compareTo(lowest) > 0) {
-            if (lastChunk === null) {
+            if (lastChunk === undefined) {
                 mergedChunks.push(chunk);
                 lastChunk = chunk;
             }
@@ -86,7 +82,37 @@ export function optimizeChunks(chunks, lowest) {
                 }
             }
         }
-    });
+    }
     return mergedChunks;
 }
+export function parsePseudoBin(bytes, offset) {
+    const lineCount = longToNumber(Long.fromBytesLE(Array.prototype.slice.call(bytes, offset, offset + 8), true));
+    return { lineCount };
+}
+export function findFirstData(firstDataLine, virtualOffset) {
+    return firstDataLine
+        ? firstDataLine.compareTo(virtualOffset) > 0
+            ? virtualOffset
+            : firstDataLine
+        : virtualOffset;
+}
+export function parseNameBytes(namesBytes, renameRefSeq = s => s) {
+    let currRefId = 0;
+    let currNameStart = 0;
+    const refIdToName = [];
+    const refNameToId = {};
+    for (let i = 0; i < namesBytes.length; i += 1) {
+        if (!namesBytes[i]) {
+            if (currNameStart < i) {
+                let refName = namesBytes.toString('utf8', currNameStart, i);
+                refName = renameRefSeq(refName);
+                refIdToName[currRefId] = refName;
+                refNameToId[refName] = currRefId;
+            }
+            currNameStart = i + 1;
+            currRefId += 1;
+        }
+    }
+    return { refNameToId, refIdToName };
+}
 //# sourceMappingURL=util.js.map

package/esm/util.js.map

@@ -1 +1 @@
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package/esm/virtualOffset.js.map

@@ -1 +1 @@
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+{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,OAAO,OAAO,aAAa;IAGhC,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;IAED,MAAM,CAAC,GAAG,CAAC,GAAG,IAAqB;QACjC,IAAI,GAAG,CAAA;QACP,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACpB,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QACf,CAAC;QACD,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC/B,IAAI,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC/B,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;YACf,CAAC;QACH,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;CACF;AACD,MAAM,UAAU,SAAS,CAAC,KAAa,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACpE,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;IACpE,CAAC;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,aAAa;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,WAAW;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,SAAS;QAC7B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,OAAO;QAC3B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,KAAK;QACzB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,EACnB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,CACzC,CAAA;AACH,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "1.1.18",
+  "version": "2.0.1",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": "GMOD/bam-js",
@@ -41,31 +41,29 @@
   "dependencies": {
     "@gmod/bgzf-filehandle": "^1.4.4",
     "abortable-promise-cache": "^1.5.0",
-    "buffer-crc32": "^0.2.13",
-    "cross-fetch": "^3.0.2",
+    "buffer-crc32": "^1.0.0",
     "generic-filehandle": "^3.0.0",
     "long": "^4.0.0",
-    "object.entries-ponyfill": "^1.0.1",
-    "quick-lru": "^2.0.0"
+    "quick-lru": "^4.0.0"
   },
   "devDependencies": {
-    "@types/buffer-crc32": "^0.2.2",
-    "@types/jest": "^29.2.4",
+    "@types/jest": "^29.5.1",
     "@types/long": "^4.0.0",
-    "@types/node": "^18.11.16",
-    "@types/quick-lru": "^2.0.0",
-    "@typescript-eslint/eslint-plugin": "^5.46.1",
-    "@typescript-eslint/parser": "^5.46.1",
-    "eslint": "^8.30.0",
-    "eslint-config-prettier": "^8.5.0",
-    "eslint-plugin-import": "^2.26.0",
-    "eslint-plugin-prettier": "^4.2.1",
-    "jest": "^29.3.1",
-    "prettier": "^2.8.1",
-    "rimraf": "^3.0.2",
-    "standard-changelog": "^2.0.27",
-    "ts-jest": "^29.0.3",
-    "typescript": "^4.9.4"
+    "@types/node": "^20.11.19",
+    "@typescript-eslint/eslint-plugin": "^7.0.2",
+    "@typescript-eslint/parser": "^7.0.2",
+    "eslint": "^8.40.0",
+    "eslint-config-prettier": "^9.1.0",
+    "eslint-plugin-import": "^2.27.5",
+    "eslint-plugin-prettier": "^5.1.3",
+    "eslint-plugin-unicorn": "^51.0.1",
+    "jest": "^29.5.0",
+    "jest-fetch-mock": "^3.0.3",
+    "prettier": "^3.2.5",
+    "rimraf": "^5.0.0",
+    "standard-changelog": "^5.0.0",
+    "ts-jest": "^29.1.0",
+    "typescript": "^5.0.4"
   },
   "publishConfig": {
     "access": "public"