@gmod/cram 1.7.1 → 1.7.3

package/CHANGELOG.md

@@ -1,3 +1,12 @@
+# v1.7.3
+
+- Fix usage of the 'b' tag under situations in CRA4 where a Uint8Array is
+  received instead of Buffer
+
+# v1.7.2
+
+- Update README.md with docs
+
 # v1.7.1
 
 - Re-export CramRecord class for typescript

package/README.md

@@ -2,14 +2,14 @@
 
 [![NPM version](https://img.shields.io/npm/v/@gmod/cram.svg?style=flat-square)](https://npmjs.org/package/@gmod/cram)
 [![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/cram-js/master.svg?style=flat-square)](https://codecov.io/gh/GMOD/cram-js/branch/master)
-[![Build Status](https://img.shields.io/github/workflow/status/GMOD/cram-js/Push/master?logo=github&style=flat-query)](https://github.com/GMOD/cram-js/actions?query=branch%3Amaster+workflow%3APush+)
+[![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/cram-js/push.yml?branch=master)](https://github.com/GMOD/cram-js/actions?query=branch%3Amaster+workflow%3APush+)
 
 Read CRAM files (indexed or unindexed) with pure JS, works in node or in the browser.
 
-- Reads CRAM 3.x and 2.x (3.1 added in v1.6.0)
-- Does not read CRAM 1.x
-- Can use .crai indexes out of the box, for efficient sequence fetching, but also has an [index API](#craiindex) that would allow use with other index types
-- Does implement bzip2 but not lzma codecs (yet); if this is important to your use case, please file an issue
+*   Reads CRAM 3.x and 2.x (3.1 added in v1.6.0)
+*   Does not read CRAM 1.x
+*   Can use .crai indexes out of the box, for efficient sequence fetching, but also has an [index API](#craiindex) that would allow use with other index types
+*   Does implement bzip2 but not lzma codecs (yet); if this is important to your use case, please file an issue
 
 ## Install
 
@@ -122,139 +122,18 @@ You can use cram-js without NPM also with the cram-bundle.js. See the example di
 
 ## API (auto-generated)
 
-- [CramRecord](#cramrecord) - format of CRAM records returned by this API
-  - [ReadFeatures](#readfeatures) - format of read features on records
-- [IndexedCramFile](#indexedcramfile) - indexed access into a CRAM file
-- [CramFile](#cramfile) - .cram API
-- [CraiIndex](#craiindex) - .crai index API
-- [Error Classes](#error-classes) - special error classes thrown by this API
+*   [CramRecord](#cramrecord) - format of CRAM records returned by this API
+    *   [ReadFeatures](#readfeatures) - format of read features on records
+*   [IndexedCramFile](#indexedcramfile) - indexed access into a CRAM file
+*   [CramFile](#cramfile) - .cram API
+*   [CraiIndex](#craiindex) - .crai index API
+*   [Error Classes](#error-classes) - special error classes thrown by this API
 
 ### CramRecord
 
 <!-- Generated by documentation.js. Update this documentation by updating the source code. -->
 
-##### Table of Contents
-
-- [CramRecord](#cramrecord)
-  - [isPaired](#ispaired)
-  - [isProperlyPaired](#isproperlypaired)
-  - [isSegmentUnmapped](#issegmentunmapped)
-  - [isMateUnmapped](#ismateunmapped)
-  - [isReverseComplemented](#isreversecomplemented)
-  - [isMateReverseComplemented](#ismatereversecomplemented)
-  - [isRead1](#isread1)
-  - [isRead2](#isread2)
-  - [isSecondary](#issecondary)
-  - [isFailedQc](#isfailedqc)
-  - [isDuplicate](#isduplicate)
-  - [isSupplementary](#issupplementary)
-  - [isDetached](#isdetached)
-  - [hasMateDownStream](#hasmatedownstream)
-  - [isPreservingQualityScores](#ispreservingqualityscores)
-  - [isUnknownBases](#isunknownbases)
-  - [getReadBases](#getreadbases)
-  - [getPairOrientation](#getpairorientation)
-  - [addReferenceSequence](#addreferencesequence)
-    - [Parameters](#parameters)
-
-#### CramRecord
-
-Class of each CRAM record returned by this API.
-
-##### isPaired
-
-Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read is paired, regardless of whether both segments are mapped
-
-##### isProperlyPaired
-
-Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read is paired, and both segments are mapped
-
-##### isSegmentUnmapped
-
-Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read itself is unmapped; conflictive with isProperlyPaired
-
-##### isMateUnmapped
-
-Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read itself is unmapped; conflictive with isProperlyPaired
-
-##### isReverseComplemented
-
-Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read is mapped to the reverse strand
-
-##### isMateReverseComplemented
-
-Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the mate is mapped to the reverse strand
-
-##### isRead1
-
-Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if this is read number 1 in a pair
-
-##### isRead2
-
-Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if this is read number 2 in a pair
-
-##### isSecondary
-
-Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if this is a secondary alignment
-
-##### isFailedQc
-
-Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if this read has failed QC checks
-
-##### isDuplicate
-
-Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read is an optical or PCR duplicate
-
-##### isSupplementary
-
-Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if this is a supplementary alignment
-
-##### isDetached
-
-Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read is detached
-
-##### hasMateDownStream
-
-Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read has a mate in this same CRAM segment
-
-##### isPreservingQualityScores
-
-Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read contains qual scores
-
-##### isUnknownBases
-
-Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read has no sequence bases
-
-##### getReadBases
-
-Get the original sequence of this read.
-
-Returns **[String](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** sequence basepairs
-
-##### getPairOrientation
-
-Get the pair orientation of a paired read. Adapted from igv.js
-
-Returns **[String](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** of paired orientatin
-
-##### addReferenceSequence
-
-Annotates this feature with the given reference sequence basepair
-information. This will add a `sub` and a `ref` item to base
-subsitution read features given the actual substituted and reference
-base pairs, and will make the `getReadSequence()` method work.
-
-###### Parameters
-
-- `refRegion` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**
-
-  - `refRegion.start` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
-  - `refRegion.end` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
-  - `refRegion.seq` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)**
-
-- `compressionScheme` **CramContainerCompressionScheme**
-
-Returns **[undefined](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/undefined)** nothing
+#### Table of Contents
 
 ### ReadFeatures
 
@@ -262,128 +141,28 @@ The feature objects appearing in the `readFeatures` member of CramRecord objects
 
 #### Static fields
 
-- **code** (`character`): One of "bqBXIDiQNSPH". See page 15 of the CRAM v3 spec for their meanings.
-- **data** (`any`): the data associated with the feature. The format of this varies depending on the feature code.
-- **pos** (`number`): location relative to the read (1-based)
-- **refPos** (`number`): location relative to the reference (1-based)
+*   **code** (`character`): One of "bqBXIDiQNSPH". See page 15 of the CRAM v3 spec for their meanings.
+*   **data** (`any`): the data associated with the feature. The format of this varies depending on the feature code.
+*   **pos** (`number`): location relative to the read (1-based)
+*   **refPos** (`number`): location relative to the reference (1-based)
 
 ### IndexedCramFile
 
 <!-- Generated by documentation.js. Update this documentation by updating the source code. -->
 
-##### Table of Contents
-
-- [constructor](#constructor)
-  - [Parameters](#parameters)
-- [getRecordsForRange](#getrecordsforrange)
-  - [Parameters](#parameters-1)
-- [hasDataForReferenceSequence](#hasdataforreferencesequence)
-  - [Parameters](#parameters-2)
-
-#### constructor
-
-##### Parameters
-
-- `args` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**
-
-  - `args.cram` **CramFile**
-  - `args.index` **Index-like** object that supports getEntriesForRange(seqId,start,end) -> Promise\[Array\[index entries]]
-  - `args.cacheSize` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?** optional maximum number of CRAM records to cache. default 20,000
-  - `args.fetchSizeLimit` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?** optional maximum number of bytes to fetch in a single getRecordsForRange call. Default 3 MiB.
-  - `args.checkSequenceMD5` **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)?** default true. if false, disables verifying the MD5
-    checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
-
-#### getRecordsForRange
-
-##### Parameters
-
-- `seq` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** numeric ID of the reference sequence
-- `start` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** start of the range of interest. 1-based closed coordinates.
-- `end` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** end of the range of interest. 1-based closed coordinates.
-- `opts` (optional, default `{}`)
-
-#### hasDataForReferenceSequence
-
-##### Parameters
-
-- `seqId` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
-
-Returns **[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)** true if the CRAM file contains data for the given
-reference sequence numerical ID
+#### Table of Contents
 
 ### CramFile
 
 <!-- Generated by documentation.js. Update this documentation by updating the source code. -->
 
-##### Table of Contents
-
-- [constructor](#constructor)
-  - [Parameters](#parameters)
-- [containerCount](#containercount)
-
-#### constructor
-
-##### Parameters
-
-- `args` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**
-
-  - `args.filehandle` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)?** a filehandle that implements the stat() and
-    read() methods of the Node filehandle API <https://nodejs.org/api/fs.html#fs_class_filehandle>
-  - `args.path` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)?** path to the cram file
-  - `args.url` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)?** url for the cram file. also supports file:// urls for local files
-  - `args.seqFetch` **[function](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Statements/function)?** a function with signature
-    `(seqId, startCoordinate, endCoordinate)` that returns a promise for a string of sequence bases
-  - `args.cacheSize` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?** optional maximum number of CRAM records to cache. default 20,000
-  - `args.checkSequenceMD5` **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)?** default true. if false, disables verifying the MD5
-    checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
-
-#### containerCount
+#### Table of Contents
 
 ### CraiIndex
 
 <!-- Generated by documentation.js. Update this documentation by updating the source code. -->
 
-##### Table of Contents
-
-- [constructor](#constructor)
-  - [Parameters](#parameters)
-- [hasDataForReferenceSequence](#hasdataforreferencesequence)
-  - [Parameters](#parameters-1)
-- [getEntriesForRange](#getentriesforrange)
-  - [Parameters](#parameters-2)
-
-#### constructor
-
-##### Parameters
-
-- `args` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**
-
-  - `args.path` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?**
-  - `args.url` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?**
-  - `args.filehandle` **FileHandle?**
-
-#### hasDataForReferenceSequence
-
-##### Parameters
-
-- `seqId` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
-
-Returns **[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)** true if the index contains entries for
-the given reference sequence ID, false otherwise
-
-#### getEntriesForRange
-
-fetch index entries for the given range
-
-##### Parameters
-
-- `seqId` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
-- `queryStart` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
-- `queryEnd` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
-
-Returns **[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)** promise for
-an array of objects of the form
-`{start, span, containerStart, sliceStart, sliceBytes }`
+#### Table of Contents
 
 ### CramUnimplementedError
 

package/dist/craiIndex.d.ts

@@ -1,12 +1,12 @@
 import { CramFileSource } from './cramFile/file';
-export declare type Slice = {
+export type Slice = {
     start: number;
     span: number;
     containerStart: number;
     sliceStart: number;
     sliceBytes: number;
 };
-declare type ParsedIndex = Record<string, Slice[]>;
+type ParsedIndex = Record<string, Slice[]>;
 export default class CraiIndex {
     private _parseCache;
     private filehandle;