bam2seq
| Crates.io | bam2seq |
| lib.rs | bam2seq |
| version | 0.1.2 |
| source | src |
| created_at | 2022-09-10 00:29:48.597567 |
| updated_at | 2022-09-10 01:13:26.63296 |
| description | Extract reads and reconstructed references from a .bam file using CIGAR and MD tags. |
| homepage | |
| repository | https://github.com/RagnarGrootKoerkamp/bam2seq |
| max_upload_size | |
| id | 662169 |
| size | 14,374 |
Ragnar Groot Koerkamp (RagnarGrootKoerkamp)
documentation
README
#+title: Bam2Seq
[[https://crates.io/crates/bam2seq][https://img.shields.io/crates/v/bam2seq.svg]] [[https://crates.io/crates/bam2seq][https://img.shields.io/crates/d/bam2seq.svg]]
This tool takes a BAM file containing CIGAR strings, reads, and MD tags,
and outputs a .seq file containing pairs of reads and reconstructed references.
** Installation
Install directly with cargo from [[https://crates.io/crates/bam2seq][crates.io]]: #+begin_src cargo install bam2seq #+end_src
Simply clone the repository, and optionally install the binary. #+begin_src git clone https://github.com/ragnargrootkoerkamp/bam2seq.git cd bam2seq cargo install --path . #+end_src
** Usage
#+begin_src
cargo run --release -- <input.bam> [<output.seq>] [--no-clip] [--min-len
input.bam:: The input BAM file.output.seq:: The output.seqfile. Defaults toinput.seq.--no-clip:: Disable trimming of soft clipped regions from the read.--min-len:: Only output (clipped) reads of at least this length.
This outputs a .seq file, which looks like this:
#+begin_src
ACTGATGA <ACAGATG read 2 <reference 2 ... #+end_src
** Links
- This is quite similar to [[https://github.com/mlafave/sam2pairwise][sam2pairwise]] but writes a simpler output format.
- All the work in the implementation is done by the [[https://docs.rs/bam/latest/bam/][BAM]] crate.