@gmod/cram 1.7.4 → 2.0.1

package/CHANGELOG.md

@@ -1,3 +1,8 @@
+# v2.0.0
+
+- Add lzma support via xz-decompress. This uses webassembly, so it is a major
+  version bump
+
 # v1.7.4
 
 - Fix import of bzip2 module
@@ -26,7 +31,8 @@
 
 # v1.6.3
 
-- Optimize CRAM parsing slightly (15% improvement on many short reads). This removes support for big endian machines
+- Optimize CRAM parsing slightly (15% improvement on many short reads). This
+  removes support for big endian machines
 - Publish src directory for sourceMap
 
 # v1.6.2
@@ -93,7 +99,8 @@
 
 # v1.4.3
 
-- Make sure mate exists for unmated pair, can exist when coordinate slices of cram file are made via samtools view
+- Make sure mate exists for unmated pair, can exist when coordinate slices of
+  cram file are made via samtools view
 
 # v1.4.2
 

package/README.md

@@ -4,12 +4,17 @@
 [![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/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
+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
+- Has preliminary support for bzip2 and lzma codecs. lzma requires the latest
+  @gmod/cram version, and uses webassembly. If you find you are unable to
+  compile it, you can try downgrading
 
 ## Install
 
@@ -118,57 +123,368 @@ run()
 // alternatively `cramFilehandle` (for the IndexedCramFile class) and `filehandle` (for the CraiIndex) can be used,  see for examples https://github.com/gmod/generic-filehandle
 ```
 
-You can use cram-js without NPM also with the cram-bundle.js. See the example directory for usage with script tag
+You can use cram-js without NPM also with the cram-bundle.js. See the example
+directory for usage with script tag
 
 ## 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
+##### 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
 
 ### ReadFeatures
 
-The feature objects appearing in the `readFeatures` member of CramRecord objects that show insertions, deletions, substitutions, etc.
+The feature objects appearing in the `readFeatures` member of CramRecord objects
+that show insertions, deletions, substitutions, etc.
 
 #### 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
+##### 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
 
 ### CramFile
 
 <!-- Generated by documentation.js. Update this documentation by updating the source code. -->
 
-#### Table of Contents
+##### 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
 
 ### CraiIndex
 
 <!-- Generated by documentation.js. Update this documentation by updating the source code. -->
 
-#### Table of Contents
+##### 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 }`
 
 ### CramUnimplementedError
 
 **Extends Error**
 
-Error caused by encountering a part of the CRAM spec that has not yet been implemented
+Error caused by encountering a part of the CRAM spec that has not yet been
+implemented
 
 ### CramMalformedError
 
@@ -184,7 +500,10 @@ An error caused by attempting to read beyond the end of the defined data.
 
 ## Academic Use
 
-This package was written with funding from the [NHGRI](http://genome.gov) as part of the [JBrowse](http://jbrowse.org) project. If you use it in an academic project that you publish, please cite the most recent JBrowse paper, which will be linked from [jbrowse.org](http://jbrowse.org).
+This package was written with funding from the [NHGRI](http://genome.gov) as
+part of the [JBrowse](http://jbrowse.org) project. If you use it in an academic
+project that you publish, please cite the most recent JBrowse paper, which will
+be linked from [jbrowse.org](http://jbrowse.org).
 
 ## License
 

package/dist/craiIndex.js.map

@@ -1 +1 @@
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