rust_htslib/bam/
index.rs

1// Copyright 2019 Johannes Köster.
2// Licensed under the MIT license (http://opensource.org/licenses/MIT)
3// This file may not be copied, modified, or distributed
4// except according to those terms.
5
6//! Module for working with BAM or CRAM indices.
7
8use std::path::Path;
9use std::ptr;
10
11use crate::errors::{Error, Result};
12use crate::htslib;
13use crate::utils;
14
15/// Index type to build.
16pub enum Type {
17    /// BAI index
18    Bai,
19    /// CSI index, with given minimum shift
20    Csi(u32),
21}
22
23/// Build a BAM index.
24pub fn build<P: AsRef<Path>>(
25    bam_path: P,
26    idx_path: Option<P>,
27    idx_type: Type,
28    n_threads: u32,
29) -> Result<()> {
30    let min_shift = match idx_type {
31        Type::Bai => 0,
32        Type::Csi(min_shift) => min_shift as i32,
33    };
34    let idx_path_cstr;
35    let idx_path_ptr = if let Some(p) = idx_path {
36        idx_path_cstr =
37            utils::path_to_cstring(&p).expect("path_to_cstring unexpectedly returned with Err");
38        idx_path_cstr.as_ptr()
39    } else {
40        ptr::null()
41    };
42    let ret = unsafe {
43        htslib::sam_index_build3(
44            utils::path_to_cstring(&bam_path).unwrap().as_ptr(),
45            idx_path_ptr,
46            min_shift,
47            n_threads as i32,
48        )
49    };
50    match ret {
51        0 => Ok(()),
52        -1 => Err(Error::BamBuildIndex),
53        -2 => Err(Error::BamOpen {
54            target: bam_path.as_ref().to_str().unwrap().to_owned(),
55        }),
56        -3 => Err(Error::BamNotIndexable),
57        -4 => Err(Error::BamWriteIndex),
58        e => panic!("unexpected error code from sam_index_build3: {}", e),
59    }
60}
61
62#[cfg(test)]
63mod tests {
64    use super::*;
65
66    #[test]
67    fn test_index_build() {
68        let test_bam = "test/test_index_build.bam";
69
70        // test BAI index creation with 1 thread
71        let idx1 = "test/results/test1.bam.bai";
72        build(test_bam, Some(idx1), Type::Bai, 1).unwrap();
73        assert!(Path::new(idx1).exists());
74
75        // test BAI index creation with 2 threads
76        let idx2 = "test/results/test2.bam.bai";
77        build(test_bam, Some(idx2), Type::Bai, 2).unwrap();
78        assert!(Path::new(idx2).exists());
79
80        // test CSI index creation with 2 threads
81        let idx3 = "test/results/test3.bam.csi";
82        build(test_bam, Some(idx3), Type::Csi(2), 2).unwrap();
83        assert!(Path::new(idx3).exists());
84
85        // test CSI index creation with 2 threads and default file name
86        build(test_bam, None, Type::Csi(5), 2).unwrap();
87        assert!(Path::new("test/test_index_build.bam.csi").exists());
88    }
89}
rust_htslib/bam/index.rs

rust_htslib/bam/
index.rs
