@gmod/cram 4.0.4 → 4.0.6

package/README.md

@@ -142,6 +142,7 @@ directory for usage with script tag
 ##### Table of Contents
 
 - [CramRecord](#cramrecord)
+  - [Parameters](#parameters)
   - [isPaired](#ispaired)
   - [isProperlyPaired](#isproperlypaired)
   - [isSegmentUnmapped](#issegmentunmapped)
@@ -161,12 +162,34 @@ directory for usage with script tag
   - [getReadBases](#getreadbases)
   - [getPairOrientation](#getpairorientation)
   - [addReferenceSequence](#addreferencesequence)
-    - [Parameters](#parameters)
+    - [Parameters](#parameters-1)
 
 #### CramRecord
 
 Class of each CRAM record returned by this API.
 
+##### Parameters
+
+- `$0` **any** 
+
+  - `$0.flags`  
+  - `$0.cramFlags`  
+  - `$0.readLength`  
+  - `$0.mappingQuality`  
+  - `$0.lengthOnRef`  
+  - `$0.qualityScores`  
+  - `$0.mateRecordNumber`  
+  - `$0.readBases`  
+  - `$0.readFeatures`  
+  - `$0.mateToUse`  
+  - `$0.readGroupId`  
+  - `$0.readName`  
+  - `$0.sequenceId`  
+  - `$0.uniqueId`  
+  - `$0.templateSize`  
+  - `$0.alignmentStart`  
+  - `$0.tags`  
+
 ##### isPaired
 
 Returns
@@ -282,23 +305,23 @@ 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
+This will add a `sub` and a `ref` item to base substitution 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)**
+  **[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)**
+    **[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)**
+    **[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)**
+    **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** 
 
-- `compressionScheme` **CramContainerCompressionScheme**
+- `compressionScheme` **CramContainerCompressionScheme** 
 
 Returns
 **[undefined](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/undefined)**
@@ -336,9 +359,9 @@ that show insertions, deletions, substitutions, etc.
 ##### Parameters
 
 - `args`
-  **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**
+  **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** 
 
-  - `args.cram` **CramFile**
+  - `args.cram` **CramFile** 
   - `args.index` **Index-like** object that supports
     getEntriesForRange(seqId,start,end) -> Promise\[Array\[index entries]]
   - `args.cacheSize`
@@ -363,14 +386,20 @@ that show insertions, deletions, substitutions, etc.
 - `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 `{}`)
+- `opts` **{viewAsPairs:
+  [boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)?,
+  pairAcrossChr:
+  [boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)?,
+  maxInsertSize:
+  [number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?}**
+  (optional, default `{}`)
 
 #### hasDataForReferenceSequence
 
 ##### Parameters
 
 - `seqId`
-  **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
+  **[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)**
@@ -383,42 +412,15 @@ ID
 
 ##### 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
 
+Returns
+**[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)<([number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)
+|
+[undefined](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/undefined))>**&#x20;
+
 ### CraiIndex
 
 <!-- Generated by documentation.js. Update this documentation by updating the source code. -->
@@ -437,20 +439,20 @@ ID
 ##### Parameters
 
 - `args`
-  **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**
+  **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**&#x20;
 
   - `args.path`
-    **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?**
+    **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?**&#x20;
   - `args.url`
-    **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?**
-  - `args.filehandle` **FileHandle?**
+    **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?**&#x20;
+  - `args.filehandle` **FileHandle?**&#x20;
 
 #### hasDataForReferenceSequence
 
 ##### Parameters
 
 - `seqId`
-  **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
+  **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**&#x20;
 
 Returns
 **[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)**
@@ -464,11 +466,11 @@ fetch index entries for the given range
 ##### Parameters
 
 - `seqId`
-  **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
+  **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**&#x20;
 - `queryStart`
-  **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
+  **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**&#x20;
 - `queryEnd`
-  **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
+  **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**&#x20;
 
 Returns
 **[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)**