diff --git a/CHANGELOG.md b/CHANGELOG.md
index f4026ce..c9460eb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,12 +1,12 @@
-
-## [1.0.40](https://github.com/GMOD/bam-js/compare/v1.0.39...v1.0.40) (2020-07-30)
+- Add htsget example
+
+## [1.0.40](https://github.com/GMOD/bam-js/compare/v1.0.39...v1.0.40) (2020-07-30)
-## [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
diff --git a/README.md b/README.md
index a9cdbe8..d1e4dac 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,6 @@
[](https://travis-ci.org/GMOD/bam-js)
[](https://codecov.io/gh/GMOD/bam-js/branch/master)
-
## Install
$ npm install --save @gmod/bam
@@ -11,11 +10,11 @@
## 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()
@@ -25,38 +24,51 @@ 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)) {
}
@@ -65,22 +77,21 @@ The getRecordsForRange simply wraps this process by concatenating chunks into an
### 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 +132,17 @@ 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)
+
+```
+
+```