Add htsget demo to README and CHANGELOG

Author: cmdcolin

CHANGELOG.md

@@ -1,12 +1,13 @@
-<a name="1.0.40"></a>
-## [1.0.40](https://github.com/GMOD/bam-js/compare/v1.0.39...v1.0.40) (2020-07-30)
+- Add htsget example
+- Support opts object to getHeader allowing things like auth headers to be passed right off the bat
 
+<a name="1.0.40"></a>
 
+## [1.0.40](https://github.com/GMOD/bam-js/compare/v1.0.39...v1.0.40) (2020-07-30)
 
 <a name="1.0.39"></a>
-## [1.0.39](https://github.com/GMOD/bam-js/compare/v1.0.38...v1.0.39) (2020-07-30)
-
 
+## [1.0.39](https://github.com/GMOD/bam-js/compare/v1.0.38...v1.0.39) (2020-07-30)
 
 - Don't use origin master in the follow-tags postpublish command for cleaner version publishing
 

README.md

@@ -3,19 +3,18 @@
 [![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)
 
-
 ## Install
 
     $ npm install --save @gmod/bam
 
 ## Usage
 
 ```js
-const {BamFile} = require('@gmod/bam'); // or import {BamFile} from '@gmod/bam'
+const { BamFile } = require('@gmod/bam') // or import {BamFile} from '@gmod/bam'
 
 const t = new BamFile({
-    bamPath: 'test.bam',
-});
+  bamPath: 'test.bam',
+})
 
 var header = await t.getHeader()
 
@@ -25,62 +24,78 @@ var records = await t.getRecordsForRange('ctgA', 0, 49999)
 
 Input are 0-based half-open coordinates (note: not the same as samtools view coordinate inputs!)
 
-## Documentation
+## Usage with htsget
 
+Since 1.0.41 we support htsget!
 
-### BAM constructor
+Here is a small code snippet for this
+
+```js
+const { HtsgetFile } = require('@gmod/bam')
+
+const ti = new HtsgetFile({
+  baseUrl: 'http://htsnexus.rnd.dnanex.us/v1/reads',
+  trackId: 'BroadHiSeqX_b37/NA12878',
+})
+await ti.getHeader()
+const records = await ti.getRecordsForRange(1, 2000000, 2000001)
+```
 
+## Documentation
+
+### BAM constructor
 
 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
-* 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
+- bamPath/baiUrl/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
 
 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
 
-
 ### async getRecordsForRange(refName, start, end, opts)
 
-* refName - a string for the chrom to fetch from
-* start - a 0 based half open start coordinate
-* end - a 0 based half open end coordinate
-* opts.signal - an AbortSignal to indicate stop processing
-* opts.viewAsPairs - re-dispatches requests to find mate pairs. default: false
-* opts.pairAcrossChr - control the viewAsPairs option behavior to pair across chromosomes. default: false
-* opts.maxInsertSize - control the viewAsPairs option behavior to limit distance within a chromosome to fetch. default: 200kb
+- refName - a string for the chrom to fetch from
+- start - a 0 based half open start coordinate
+- end - a 0 based half open end coordinate
+- opts.signal - an AbortSignal to indicate stop processing
+- opts.viewAsPairs - re-dispatches requests to find mate pairs. default: false
+- opts.pairAcrossChr - control the viewAsPairs option behavior to pair across chromosomes. default: false
+- opts.maxInsertSize - control the viewAsPairs option behavior to limit distance within a chromosome to fetch. default: 200kb
 
+### async \*streamRecordsForRange(refName, start, end, opts)
 
-### async *streamRecordsForRange(refName, start, end, opts)
-
-This is a async generator function that takes the same signature as getRecordsForRange but results can be processed using 
+This is a async generator function that takes the same signature as getRecordsForRange but results can be processed using
 
     for await(const chunk of file.streamRecordsForRange(refName, start, end, opts)) {
     }
 
 The getRecordsForRange simply wraps this process by concatenating chunks into an array
 
+### async getHeader(opts: {....anything to pass to generic-filehandle opts})
+
+This obtains the header from HtsgetFile or BamFile. Retrieves BAM file and BAI/CSI header if applicable, or API request for refnames from htsget
+
 ### async indexCov(refName, start, end)
 
-* refName - a string for the chrom to fetch from
-* start - a 0 based half open start coordinate (optional)
-* end - a 0 based half open end coordinate (optional)
+- refName - a string for the chrom to fetch from
+- start - a 0 based half open start coordinate (optional)
+- end - a 0 based half open end coordinate (optional)
 
 Returns features of the form {start, end, score} containing estimated feature density across 16kb windows in the genome
 
-
 ### async lineCount(refName)
 
-* refName - a string for the chrom to fetch from
+- refName - a string for the chrom to fetch from
 
 Returns number of features on refName, uses special pseudo-bin from the BAI/CSI index (e.g. bin 37450 from bai, returning n_mapped from SAM spec pdf) or -1 if refName not exist in sample
 
 ### async hasRefSeq(refName)
 
-* refName - a string for the chrom to check
+- refName - a string for the chrom to check
 
 Returns whether we have this refName in the sample
 
@@ -121,14 +136,17 @@ Example
 BAM tags such as MD can be obtained via
 
     feature.get('MD')
-    
+
 A full list of tags that can be obtained can be obtained via
 
     feature._tags()
-    
-    
+
 The feature format may change in future versions to be more raw data records, but this will be a major version bump
 
 ## License
 
 MIT © [Colin Diesh](https://github.com/cmdcolin)
+
+```
+
+```