@gmod/cram 1.5.7 → 1.6.1

package/CHANGELOG.md

@@ -0,0 +1,86 @@
+# v1.6.1
+
+- Explicitly use pako for browser bundle to help avoid buggy zlib polyfills
+
+# v1.6.0
+
+- Support CRAMv3.1 (thanks to @jkbonfield for contributing!)
+- Support bzip codec
+- Remove localFile from the browser bundle using "browser" package.json field
+- Add esm module field in package.json
+
+# v1.5.9
+
+- Fix CRAM not downloading proper records for long reads (pt2, PR #84)
+
+# v1.5.8
+
+- Fix CRAM not downloading proper records for long reads (pt1, PR #85)
+
+# v1.5.7
+
+- Add getHeaderText to CRAM to get SAM header
+
+# v1.5.6
+
+- Remove unnecessary rethor win tinyMemoize error handler
+- Avoid uncaught promise from constructor
+
+# v1.5.5
+
+- Fix ability to reload CRAM file after failure
+- Check if BAI file incorrectly submitted as index for CRAM
+
+# v1.5.4
+
+- Fix handling of hard clipping
+
+# v1.5.3
+
+- Improved README
+- Upgrade to babel 7
+- Upgrade @gmod/binary-parser
+- Add fix for 'b', 'q', and 'Q' readFeatures
+
+# v1.5.2
+
+- Fix off-by-one error in range query
+- Add webpack cram-bundle.js
+
+# v1.5.1
+
+- Add fix for when mate is unmapped
+
+# v1.5.0
+
+- Add lossy-names support
+- Fix for mate strand
+
+# v1.4.3
+
+- Make sure mate exists for unmated pair, can exist when coordinate slices of cram file are made via samtools view
+
+# v1.4.2
+
+- Switch to es6-promisify for ie11
+- Switch to quick-lru instead of lru-cache for ie11
+
+# v1.4.1
+
+- Add maxInsertSize for viewAsPairs
+
+# v1.4.0
+
+- Add viewAsPairs implementation
+
+# v1.3.0
+
+- Fix tests in node 6
+- Make cram record unique IDs start at 1 instead of 0 to always be truthy
+- Implement gamma and subexp codecs
+
+# v1.2.0
+
+- Add `getReadBases` docs
+- Rewrite seq calculation to be much faster
+- Implement ref fetching for multi-ref slices

package/README.md

@@ -1,15 +1,15 @@
 # @gmod/cram
 
-[![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/cram.svg?style=flat-square)](https://npmjs.org/package/@gmod/cram)
-[![Build Status](https://img.shields.io/travis/GMOD/cram-js/master.svg?style=flat-square)](https://travis-ci.org/GMOD/cram-js) [![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) [![Greenkeeper badge](https://badges.greenkeeper.io/GMOD/cram-js.svg)](https://greenkeeper.io/)
+[![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+)
 
 Read CRAM files (indexed or unindexed) with pure JS, works in node or in the browser.
 
--   Reads CRAM 3.x and 2.x
--   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 not implement bzip2 or lzma codecs (yet), as these are rarely used in-the-wild; 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
 
@@ -24,101 +24,142 @@ $ yarn add @gmod/cram
 ```js
 const { IndexedCramFile, CramFile, CraiIndex } = require('@gmod/cram')
 
-//Use indexedfasta library for seqFetch, if using local file (see below)
-const { IndexedFasta, BgzipIndexedFasta } = require('@gmod/indexedfasta') 
-
+// Use indexedfasta library for seqFetch, if using local file (see below)
+const { IndexedFasta, BgzipIndexedFasta } = require('@gmod/indexedfasta')
 
+// this uses local file paths for node.js for IndexedFasta, for usages using
+// remote URLs see indexedfasta docs for filehandles and
+// https://github.com/gmod/generic-filehandle
 const t = new IndexedFasta({
   path: '/filesystem/yourfile.fa',
   faiPath: '/filesystem/yourfile.fa.fai',
-});
-
-
-// open local files
-const indexedFile = new IndexedCramFile({
-  cramPath: '/filesystem/yourfile.cram',
-  index: new CraiIndex({
-    path: '/filesystem/yourfile.cram.crai'),
-  }),
-  seqFetch: async (seqId, start, end) => {
-    // note: 
-    // * seqFetch should return a promise for a string, in this instance retrieved from IndexedFasta
-    // * we use start-1 because cram-js uses 1-based but IndexedFasta uses 0-based coordinates
-    // * the seqId is a numeric identifier
-    return seq = await t.getSequence(seqId, start-1, end)
-    }
-  },
-  checkSequenceMD5: false,
 })
 
 // example of fetching records from an indexed CRAM file.
-// NOTE: only numeric IDs for the reference sequence are accepted. 
-// For indexedfasta the numeric ID is the order in which the sequence names appear in the header
+// NOTE: only numeric IDs for the reference sequence are accepted.
+// For indexedfasta the numeric ID is the order in which the sequence names
+// appear in the header
 
 // Wrap in an async and then run
-run = async() => {
-  const records = await indexedFile.getRecordsForRange(0, 10000, 20000)
+run = async () => {
+  const idToName = []
+  const nameToId = {}
+
+  // example opening local files on node.js
+  // can also pass `cramUrl` (for the IndexedCramFile class), and `url` (for
+  // the CraiIndex) params to open remote URLs
+  //
+  // alternatively `cramFilehandle` (for the IndexedCramFile class) and
+  // `filehandle` (for the CraiIndex) can be used,  see for examples
+  // https://github.com/gmod/generic-filehandle
+
+  const indexedFile = new IndexedCramFile({
+    cramPath: '/filesystem/yourfile.cram',
+    //or
+    //cramUrl: 'url/to/file.cram'
+    //cramFilehandle: a generic-filehandle or similar filehandle
+    index: new CraiIndex({
+      path: '/filesystem/yourfile.cram.crai',
+      // or
+      // url: 'url/to/file.cram.crai'
+      // filehandle: a generic-filehandle or similar filehandle
+    }),
+    seqFetch: async (seqId, start, end) => {
+      // note:
+      // * seqFetch should return a promise for a string, in this instance retrieved from IndexedFasta
+      // * we use start-1 because cram-js uses 1-based but IndexedFasta uses 0-based coordinates
+      // * the seqId is a numeric identifier, so we convert it back to a name with idToName
+      // * you can return an empty string from this function for testing if you want, but you may not get proper interpretation of record.readFeatures
+      return t.getSequence(idToName[seqId], start - 1, end)
+    },
+    checkSequenceMD5: false,
+  })
+  const samHeader = await indexedFile.cram.getSamHeader()
+
+  // use the @SQ lines in the header to figure out the
+  // mapping between ref ref ID numbers and names
+
+  const sqLines = samHeader.filter(l => l.tag === 'SQ')
+  sqLines.forEach((sqLine, refId) => {
+    sqLine.data.forEach(item => {
+      if (item.tag === 'SN') {
+        // this is the ref name
+        const refName = item.value
+        nameToId[refName] = refId
+        idToName[refId] = refName
+      }
+    })
+  })
+
+  const records = await indexedFile.getRecordsForRange(
+    nameToId['chr1'],
+    10000,
+    20000,
+  )
   records.forEach(record => {
     console.log(`got a record named ${record.readName}`)
-    record.readFeatures.forEach(({ code, pos, refPos, ref, sub }) => {
-      // process the "read features". this can be used similar to
-      // CIGAR/MD strings in SAM. see CRAM specs for more details.
-      if (code === 'X')
-        console.log(
-          `${
-            record.readName
-          } shows a base substitution of ${ref}->${sub} at ${refPos}`,
-        )
-    })
+    if (record.readFeatures != undefined) {
+      record.readFeatures.forEach(({ code, pos, refPos, ref, sub }) => {
+        // process the read features. this can be used similar to
+        // CIGAR/MD strings in SAM. see CRAM specs for more details.
+        if (code === 'X') {
+          console.log(
+            `${record.readName} shows a base substitution of ${ref}->${sub} at ${refPos}`,
+          )
+        }
+      })
+    }
   })
 }
 
 run()
 
-
 // can also pass `cramUrl` (for the IndexedCramFile class), and `url` (for the CraiIndex) params to open remote URLs
 // 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
+
 ## 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
 
-These are the record objects returned by this API. Much of the data
-is stored in them as simple object entries, but there are some accessor
-methods used for conveniently getting the values of each of the flags in
-the `flags` and `cramFlags` fields.
-
-#### Static fields
-
-- **flags** (`number`): the SAM bit-flags field, see the SAM spec for interpretation. Some of the `is*` methods below interpret this field.
-- **cramFlags** (`number`): the CRAM-specific bit-flags field, see the CRAM spec for interpretation. Some of the `is*` methods below interpret this field.
-- **sequenceId** (`number`): the ID number of the record's reference sequence
-- **readLength** (`number`): length of the read in bases
-- **alignmentStart** (`number`): start coordinate of the alignment on the reference in 1-based closed coordinates
-- **readGroupId** (`number`): ID number of the read group, or -1 if none
-- **readName** (`number`): name of the read (string)
-- **templateSize** (`number`): for paired sequencing, the total size of the template
-- **readFeatures** (`array[ReadFeature]`): array of read features showing insertions, deletions, mismatches, etc. See [ReadFeatures](#readfeatures) for their format.
-- **lengthOnRef** (`number`): span of the alignment along the reference sequence
-- **mappingQuality** (`number`): SAM mapping quality
-- **qualityScores** (`array[number]`): array of numeric quality scores
-- **uniqueId** (`number`): unique ID number of the record within the file
-- **mate** (`object`)
-  - **flags** (`number`): CRAM mapping flags for the mate. See CRAM spec for interpretation. Some of the `is*` methods below interpret this field.
-  - **sequenceId** (`number`): reference sequence ID for the mate mapping
-  - **alignmentStart** (`number`): start coordinate of the mate mapping. 1-based coordinates.
-
 <!-- Generated by documentation.js. Update this documentation by updating the source code. -->
 
-#### Methods
+##### 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
 
@@ -190,6 +231,12 @@ 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
@@ -197,13 +244,15 @@ 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**
+###### 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** 
+- `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
 
@@ -220,41 +269,44 @@ The feature objects appearing in the `readFeatures` member of CramRecord objects
 
 ### IndexedCramFile
 
-The pairing of an index and a CramFile. Supports efficient fetching of records for sections of reference sequences.
-
 <!-- Generated by documentation.js. Update this documentation by updating the source code. -->
 
 ##### Table of Contents
 
--   [constructor](#constructor)
--   [getRecordsForRange](#getrecordsforrange)
--   [hasDataForReferenceSequence](#hasdataforreferencesequence)
+- [constructor](#constructor)
+  - [Parameters](#parameters)
+- [getRecordsForRange](#getrecordsforrange)
+  - [Parameters](#parameters-1)
+- [hasDataForReferenceSequence](#hasdataforreferencesequence)
+  - [Parameters](#parameters-2)
 
 #### constructor
 
-**Parameters**
+##### 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.
+- `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**
+##### 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.
+- `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**
+##### Parameters
 
--   `seqId` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** 
+- `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
@@ -265,54 +317,56 @@ reference sequence numerical ID
 
 ##### Table of Contents
 
--   [constructor](#constructor)
--   [containerCount](#containercount)
+- [constructor](#constructor)
+  - [Parameters](#parameters)
+- [containerCount](#containercount)
 
 #### constructor
 
-**Parameters**
+##### 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.
+- `args` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**
 
-#### containerCount
+  - `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.
 
-Returns **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** the number of containers in the file
+#### containerCount
 
 ### CraiIndex
 
-Represents a .crai index.
-
 <!-- Generated by documentation.js. Update this documentation by updating the source code. -->
 
 ##### Table of Contents
 
--   [constructor](#constructor)
--   [hasDataForReferenceSequence](#hasdataforreferencesequence)
--   [getEntriesForRange](#getentriesforrange)
+- [constructor](#constructor)
+  - [Parameters](#parameters)
+- [hasDataForReferenceSequence](#hasdataforreferencesequence)
+  - [Parameters](#parameters-1)
+- [getEntriesForRange](#getentriesforrange)
+  - [Parameters](#parameters-2)
 
 #### constructor
 
-**Parameters**
+##### 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?** 
+- `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**
+##### Parameters
 
--   `seqId` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** 
+- `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
@@ -321,60 +375,16 @@ the given reference sequence ID, false otherwise
 
 fetch index entries for the given range
 
-**Parameters**
+##### 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)** 
+- `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 }`
 
-#### Error Classes
-
-`@gmod/cram/errors` contains some special error classes thrown by cram-js. A list of the error classes is below.
-
-<!-- Generated by documentation.js. Update this documentation by updating the source code. -->
-
-##### Table of Contents
-
--   [CramUnimplementedError](#cramunimplementederror)
--   [CramMalformedError](#crammalformederror)
--   [CramBufferOverrunError](#crambufferoverrunerror)
--   [CramSizeLimitError](#cramsizelimiterror)
--   [CramArgumentError](#cramargumenterror)
-
-#### CramUnimplementedError
-
-**Extends Error**
-
-Error caused by encountering a part of the CRAM spec that has not yet been implemented
-
-#### CramMalformedError
-
-**Extends CramError**
-
-An error caused by malformed data.
-
-#### CramBufferOverrunError
-
-**Extends CramMalformedError**
-
-An error caused by attempting to read beyond the end of the defined data.
-
-#### CramSizeLimitError
-
-**Extends CramError**
-
-An error caused by data being too big, exceeding a size limit.
-
-#### CramArgumentError
-
-**Extends CramError**
-
-An invalid argument was supplied to a cram-js method or object.
-
 ### CramUnimplementedError
 
 **Extends Error**

package/dist/craiIndex.d.ts

@@ -0,0 +1,37 @@
+export default class CraiIndex {
+    /**
+     *
+     * @param {object} args
+     * @param {string} [args.path]
+     * @param {string} [args.url]
+     * @param {FileHandle} [args.filehandle]
+     */
+    constructor(args: {
+        path?: string | undefined;
+        url?: string | undefined;
+        filehandle?: any;
+    });
+    _parseCache: AbortablePromiseCache<any, any>;
+    readFile: any;
+    parseIndex(): any;
+    getIndex(opts?: {}): Promise<any>;
+    /**
+     * @param {number} seqId
+     * @returns {Promise} true if the index contains entries for
+     * the given reference sequence ID, false otherwise
+     */
+    hasDataForReferenceSequence(seqId: number): Promise<any>;
+    /**
+     * fetch index entries for the given range
+     *
+     * @param {number} seqId
+     * @param {number} queryStart
+     * @param {number} queryEnd
+     *
+     * @returns {Promise} promise for
+     * an array of objects of the form
+     * `{start, span, containerStart, sliceStart, sliceBytes }`
+     */
+    getEntriesForRange(seqId: number, queryStart: number, queryEnd: number): Promise<any>;
+}
+import AbortablePromiseCache from "abortable-promise-cache";