libsais 0.2.0

Bindings to the C library libsais for suffix array construction
Documentation 
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use libsais::bwt::{AuxIndicesSamplingRate, Bwt};
use libsais::context::UnBwtContext;
use libsais::{BwtConstruction, suffix_array::ExtraSpace};

mod common;

use common::*;

#[test]
fn empty_text_bwt_unbwt() {
    let bwt: Bwt<u8, _> = BwtConstruction::for_text(&[])
        .with_owned_temporary_array_buffer32()
        .single_threaded()
        .run()
        .expect("libsais bwt should run without an error");

    assert_eq!(0, bwt.primary_index());

    assert!(is_libsais_bwt::<u8, i32>(&[], &[], bwt.bwt()));

    let text = bwt
        .unbwt()
        .with_owned_temporary_array_buffer32()
        .single_threaded()
        .run()
        .expect("libsais unbwt should run without an error");

    assert!(text.as_slice().is_empty());
}

#[test]
fn unbwt() {
    let (text, _, mut frequency_table, mut ctx) = setup_basic_example();

    let mut construction = BwtConstruction::for_text(text)
        .with_owned_temporary_array_buffer_and_extra_space32(ExtraSpace::None)
        .single_threaded()
        .with_context(&mut ctx);

    // SAFETY: the frequency table defined in the example is valid
    unsafe {
        construction = construction.with_frequency_table(&mut frequency_table);
    }

    let bwt = construction
        .run()
        .expect("libsais bwt should run without errors");

    let mut unbwt_ctx = UnBwtContext::new_single_threaded();

    let mut unbwt = bwt
        .unbwt()
        .with_owned_temporary_array_buffer32()
        .single_threaded()
        .with_context(&mut unbwt_ctx);

    // SAFETY: the frequency table defined in the example is valid
    unsafe {
        unbwt = unbwt.with_frequency_table(&mut frequency_table);
    }

    let recovered_text = unbwt
        .run()
        .expect("libsais unbwt should run without errors");

    assert_eq!(recovered_text.as_slice(), text);
}

#[test]
fn unbwt_in_place_with_aux() {
    let (text, _, mut frequency_table, mut ctx) = setup_basic_example();
    let mut text_then_bwt_then_text = text.to_vec();

    let mut construction = BwtConstruction::replace_text(&mut text_then_bwt_then_text)
        .with_owned_temporary_array_buffer32()
        .single_threaded()
        .with_context(&mut ctx)
        .with_aux_indices(AuxIndicesSamplingRate::from(2));

    // SAFETY: the frequency table defined in the example is valid
    unsafe {
        construction = construction.with_frequency_table(&mut frequency_table);
    }

    let bwt = construction
        .run()
        .expect("libsais bwt should run without errors");

    let mut unbwt_ctx = UnBwtContext::new_single_threaded();

    let mut unbwt = bwt
        .unbwt()
        .replace_bwt()
        .single_threaded()
        .with_context(&mut unbwt_ctx);

    // SAFETY: the frequency table defined in the example is valid
    unsafe {
        unbwt = unbwt.with_frequency_table(&mut frequency_table);
    }

    let _ = unbwt
        .run()
        .expect("libsais unbwt should run without errors");

    assert_eq!(&text_then_bwt_then_text, text);
}