msbwt2 0.3.2

msbwt2 - multi-string BWT query library
Documentation 
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# msbwt2
The intent of crate is to provide Rust functionality for querying a Multi-String BWT (MSBWT), and is mostly based on the same methodology used by the original [msbwt](https://github.com/holtjma/msbwt).

NOTE: This is very much a work-in-progress and currently only being updated as a side project during spare time.
If you have any feature requests, feel free to submit a new issue on GitHub.
Here is a current list of planned additions:

1. Incorporate the high-memory BWT implementation from `fmlrc2`
2. Add some more query functionality
3. Improve the performance of the built-in BWT construction tool (`msbwt2-build`)

## Installation
All installation options assume you have installed [Rust](https://www.rust-lang.org) along with the `cargo` crate manager for Rust.

### From Cargo
```bash
cargo install msbwt2
msbwt2-convert -h
```

### From GitHub
```bash 
git clone https://github.com/HudsonAlpha/rust-msbwt.git
cd rust-msbwt
#testing optional
cargo test --release
cargo build --release
./target/release/msbwt2-convert -h
```

## Usage
### MSBWT Building
The Multi-String Burrows Wheeler Transform (MSBWT or BWT) must be built prior to performing any queries. 
Currently, there are two ways to build the BWT with identical results:
1. Using the built-in `msbwt2-build` tool. 
This approach will accept any combination of FASTQ or FASTA files that may be gzip-compressed.  
This method tends to be slower currently and is not parallelized (we hope to improve both of these over time).
However, it is easier to use with different file types requires only `msbwt2` to be installed:
```
msbwt2-build \
    -o comp_msbwt.npy \
    reads.fq.gz [reads2.fq.gz ...]
```
2. Using an external tool and feeding that to `msbwt2-convert`. This approach tends to be faster currently.  However, the following command is more complex, less flexible file typing (requiring FASTQ in this example), and requires the [ropebwt2](https://github.com/lh3/ropebwt2) executable (or a similar tool) to be installed:
```
gunzip -c reads.fq.gz [read2.fq.gz ...] | \
    awk 'NR % 4 == 2' | \
    sort | \
    tr NT TN | \
    ropebwt2 -LR | \
    tr NT TN | \
    msbwt2-convert comp_msbwt.npy
```

### Queries
The general use case of the library is k-mer queries, which can be performed as follows:
```rust
use msbwt2::msbwt_core::BWT;
use msbwt2::rle_bwt::RleBWT;
use msbwt2::string_util;
let mut bwt = RleBWT::new();
let filename: String = "test_data/two_string.npy".to_string();
bwt.load_numpy_file(&filename);
assert_eq!(bwt.count_kmer(&string_util::convert_stoi(&"ACGT")), 1);
```

## Reference
`msbwt2` does not currently have a pre-print or paper. If you use `msbwt2`, please cite the one of the `msbwt` papers:

[Holt, James, and Leonard McMillan. "Merging of multi-string BWTs with applications." Bioinformatics 30.24 (2014): 3524-3531.](https://doi.org/10.1093/bioinformatics/btu584)

[Holt, James, and Leonard McMillan. "Constructing Burrows-Wheeler transforms of large string collections via merging." Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. 2014.](https://doi.org/10.1145/2649387.2649431)

## License
Licensed under either of

 * Apache License, Version 2.0
   ([LICENSE-APACHE](LICENSE-APACHE) or http://www.apache.org/licenses/LICENSE-2.0)
 * MIT license
   ([LICENSE-MIT](LICENSE-MIT) or http://opensource.org/licenses/MIT)

at your option.

## Contribution
Unless you explicitly state otherwise, any contribution intentionally submitted
for inclusion in the work by you, as defined in the Apache-2.0 license, shall be
dual licensed as above, without any additional terms or conditions.