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https://github.com/chrovis/cljam
A DNA Sequence Alignment/Map (SAM) library for Clojure
https://github.com/chrovis/cljam
2bit bam bcf bed bigwig bioinformatics clojure cram fasta fastq genomics gff sam vcf wig
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A DNA Sequence Alignment/Map (SAM) library for Clojure
- Host: GitHub
- URL: https://github.com/chrovis/cljam
- Owner: chrovis
- License: apache-2.0
- Created: 2014-01-08T09:52:14.000Z (almost 11 years ago)
- Default Branch: master
- Last Pushed: 2024-10-30T06:22:38.000Z (16 days ago)
- Last Synced: 2024-10-30T08:41:23.698Z (16 days ago)
- Topics: 2bit, bam, bcf, bed, bigwig, bioinformatics, clojure, cram, fasta, fastq, genomics, gff, sam, vcf, wig
- Language: Clojure
- Homepage: https://chrovis.github.io/cljam
- Size: 36.2 MB
- Stars: 90
- Watchers: 11
- Forks: 12
- Open Issues: 9
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
- Codeowners: .github/CODEOWNERS
Awesome Lists containing this project
README
# cljam
A DNA Sequence Alignment/Map (SAM) library for Clojure. [[API Reference]][api-reference] [[Annotated Source]][annotated-source]
[](https://clojars.org/cljam)
[](https://github.com/chrovis/cljam/actions)
[](https://codecov.io/gh/chrovis/cljam)
## Installation
cljam is available as a Maven artifact from [Clojars](https://clojars.org/cljam).
Clojure CLI/deps.edn:
```clojure
cljam {:mvn/version "0.8.5"}
```
Leiningen/Boot:
```clojure
[cljam "0.8.5"]
```
## Breaking changes in 0.8.0
* `cljam.io.tabix` is rewritten. [#180](https://github.com/chrovis/cljam/pull/180)
* `cljam.io.bam-index.writer/pos->lidx-offset` is moved to `cljam.io.util.bin/pos->lidx-offset`. [#180](https://github.com/chrovis/cljam/pull/180)
* `cljam.io.sam.util/reg->bin` is moved to `cljam.io.util.bin/reg->bin`. Also, a coordinate system of its argument is changed from 0-based half-open to 1-based fully-closed. [#190](https://github.com/chrovis/cljam/pull/190)
## Getting started
To read a SAM/BAM format file,
```clojure
(require '[cljam.io.sam :as sam])
;; Open a file
(with-open [r (sam/reader "path/to/file.bam")]
;; Retrieve header
(sam/read-header r)
;; Retrieve alignments
(doall (take 5 (sam/read-alignments r))))
```
To create a sorted file,
```clojure
(require '[cljam.io.sam :as sam]
'[cljam.algo.sorter :as sorter])
(with-open [r (sam/reader "path/to/file.bam")
w (sam/writer "path/to/sorted.bam")]
;; Sort by chromosomal coordinates
(sorter/sort-by-pos r w))
```
To create a BAM index file,
```clojure
(require '[cljam.algo.bam-indexer :as bai])
;; Create a new BAM index file
(bai/create-index "path/to/sorted.bam" "path/to/sorted.bam.bai")
```
To calculate coverage depth for a BAM file,
```clojure
(require '[cljam.io.sam :as sam]
'[cljam.algo.depth :as depth])
(with-open [r (sam/reader "path/to/sorted.bam")]
;; Pileup "chr1" alignments
(depth/depth r {:chr "chr1", :start 1, :end 10}))
;;=> (0 0 0 0 0 0 1 1 3 3)
```
If you are Clojure beginner, read [Getting Started for Clojure Beginners](https://github.com/chrovis/cljam/wiki/Getting-Started-for-Clojure-Beginners).
## Command-line tool
cljam provides a command-line tool to use the features easily.
**NOTICE**
The command-line tool functionality will be removed from cljam on the next
release. The functionality has been already integrated into
[Gnife](https://github.com/chrovis/gnife), which is a pure command-line tool.
### Executable installation
`lein bin` creates standalone console executable into `target` directory.
```console
$ lein bin
Creating standalone executable: /path/to/cljam/target/cljam
```
Copy the executable `cljam` somewhere in your `$PATH`.
### Usage
All commands are displayed by `cljam -h`, and detailed help for each command are displayed by `cljam [cmd] -h`.
```console
$ cljam view -h
```
For example, to display contents of a SAM file including the header,
```console
$ cljam view --header path/to/file.sam
```
See [command-line tool manual](https://github.com/chrovis/cljam/wiki/Command-line-tool) for more information.
## Development
### Test
To run tests,
- `lein test` for basic tests,
- `lein test :slow` for slow tests with local resources,
- `lein test :remote` for tests with remote resources.
To get coverage
```console
$ lein cloverage
```
And open `target/coverage/index.html`.
### Generating document
cljam uses [Codox](https://github.com/weavejester/codox) for API reference and
[Marginalia](https://github.com/gdeer81/marginalia) for annotated source code.
```console
$ lein docs
```
generates these documents in `target/docs` and `target/literate` directories.
## Citing cljam
T. Takeuchi, A. Yamada, T. Aoki, and K. Nishimura. [cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing](http://dx.doi.org/10.1186/s13029-016-0058-6). Source Code for Biology and Medicine, Vol. 11, No. 1, pp. 1-4, 2016.
## Contributors
Sorted by first commit.
- Toshiki Takeuchi ([@totakke](https://github.com/totakke))
- Takashi Aoki ([@federkasten](https://github.com/federkasten))
- Atsuo Yamada ([@ayamada](https://github.com/ayamada))
- Jun Imura ([@alumi](https://github.com/alumi))
- Shogo Ohta ([@athos](https://github.com/athos))
- Shunya Kawabata ([@r6eve](https://github.com/r6eve))
- Yuji Ito ([@yito88](https://github.com/yito88))
- Akira Inoue ([@niyarin](https://github.com/niyarin))
- Atsushi Kitahara ([@xckitahara](https://github.com/xckitahara))
- Kei Komazaki ([@k-kom](https://github.com/k-kom))
- Tomoki Matsuda ([@matsutomo81](https://github.com/matsutomo81))
- Ryutaro Nagata ([@nuggetoriniku](https://github.com/nuggetoriniku))
## License
Copyright 2013-2024 [Xcoo, Inc.](https://xcoo.jp/)
Licensed under the [Apache License, Version 2.0](LICENSE).
[api-reference]: https://chrovis.github.io/cljam/docs
[annotated-source]: https://chrovis.github.io/cljam/literate