@gmod/bam 1.1.6 → 1.1.10

package/CHANGELOG.md

@@ -1,8 +1,36 @@
-<a name="1.1.6"></a>
-## [1.1.6](https://github.com/GMOD/bam-js/compare/v1.1.5...v1.1.6) (2021-02-20)
+<a name="1.1.10"></a>
+## [1.1.10](https://github.com/GMOD/bam-js/compare/v1.1.9...v1.1.10) (2022-01-18)
+
+
+
+- Make _refID and flags public fields
+- Small internal changes to the handling of opts
+
+<a name="1.1.9"></a>
+## [1.1.9](https://github.com/GMOD/bam-js/compare/v1.1.8...v1.1.9) (2021-12-14)
+
+
+
+- Add ESM module export in package.json (smaller bundle size for consumers)
+- Cache BAI readFile result for compatibility with node.js native filehandles (which otherwise fail if re-reading the filehandle twice)
 
+<a name="1.1.8"></a>
+## [1.1.8](https://github.com/GMOD/bam-js/compare/v1.1.7...v1.1.8) (2021-05-21)
 
 
+
+- Fix types for yieldThreadTime
+
+<a name="1.1.7"></a>
+
+## [1.1.7](https://github.com/GMOD/bam-js/compare/v1.1.6...v1.1.7) (2021-05-21)
+
+- New param yieldThreadTime to constructor to yield while processing
+
+<a name="1.1.6"></a>
+
+## [1.1.6](https://github.com/GMOD/bam-js/compare/v1.1.5...v1.1.6) (2021-02-20)
+
 - Add qualRaw function on records for getting raw qual score array instead of string
 
 <a name="1.1.5"></a>

package/README.md

@@ -1,7 +1,6 @@
-[![Generated with nod](https://img.shields.io/badge/generator-nod-2196F3.svg?style=flat-square)](https://github.com/diegohaz/nod)
 [![NPM version](https://img.shields.io/npm/v/@gmod/bam.svg?style=flat-square)](https://npmjs.org/package/@gmod/bam)
-[![Build Status](https://img.shields.io/travis/GMOD/bam-js/master.svg?style=flat-square)](https://travis-ci.org/GMOD/bam-js)
 [![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/bam-js/master.svg?style=flat-square)](https://codecov.io/gh/GMOD/bam-js/branch/master)
+[![Build Status](https://img.shields.io/github/workflow/status/GMOD/bam-js/Push/master?logo=github&style=flat-query)](https://github.com/GMOD/bam-js/actions?query=branch%3Amaster+workflow%3APush+)
 
 ## Install
 
@@ -47,12 +46,13 @@ const records = await ti.getRecordsForRange(1, 2000000, 2000001)
 
 The BAM class constructor accepts arguments
 
-- bamPath/baiUrl/bamFilehandle - a string file path to a local file or a class object with a read method
+- bamPath/bamUrl/bamFilehandle - a string file path to a local file or a class object with a read method
 - csiPath/csiUrl/csiFilehandle - a CSI index for the BAM file, required for long chromosomes greater than 2^29 in length
 - baiPath/baiUrl/baiFilehandle - a BAI index for the BAM file
 - fetchSizeLimit - total size of the number of chunks being fetched at once. default: ~50MB
 - chunkSizeLimit - size limit on any individual chunk. default: ~10MB
 - cacheSize - limit on number of chunks to cache. default: 50
+- yieldThreadTime - the interval at which the code yields to the main thread when it is parsing a lot of data. default: 100ms. Set to 0 to performed no yielding
 
 Note: filehandles implement the Filehandle interface from https://www.npmjs.com/package/generic-filehandle. This module offers the path and url arguments as convenience methods for supplying the LocalFile and RemoteFile
 

package/dist/bai.d.ts

@@ -3,10 +3,12 @@ import Chunk from './chunk';
 import IndexFile from './indexFile';
 import { BaseOpts } from './util';
 export default class BAI extends IndexFile {
+    baiP?: Promise<Buffer>;
     parsePseudoBin(bytes: Buffer, offset: number): {
         lineCount: number;
     };
     lineCount(refId: number, opts?: BaseOpts): Promise<any>;
+    fetchBai(opts?: BaseOpts): Promise<Buffer>;
     _parse(opts?: BaseOpts): Promise<{
         [key: string]: any;
     }>;