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feat: Add rust_htslib::bcf::index::build (#408)
* Add rust_htslib::bcf::index::build, to build a bcf/vcf index. * Add doctests for vcf + bcf index building.
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use crate::{htslib, utils}; | ||
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#[derive(Debug)] | ||
pub struct BcfBuildError { | ||
pub msg: String, | ||
} | ||
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/// Index type to build. | ||
pub enum Type { | ||
/// Tabix index | ||
Tbx, | ||
/// CSI index, with given minimum shift | ||
Csi(u32), | ||
} | ||
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impl Type { | ||
fn min_shift(&self) -> i32 { | ||
match self { | ||
Self::Tbx => 0, | ||
Self::Csi(x) => *x as i32, | ||
} | ||
} | ||
} | ||
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impl BcfBuildError { | ||
pub fn error_message(error: i32) -> &'static str { | ||
match error { | ||
-1 => "indexing failed", | ||
-2 => "opening @fn failed", | ||
-3 => "format not indexable", | ||
-4 => "failed to create and/or save the index", | ||
_ => "unknown error", | ||
} | ||
} | ||
} | ||
impl std::error::Error for BcfBuildError {} | ||
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impl std::fmt::Display for BcfBuildError { | ||
fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { | ||
write!(f, "BcfBuildError{{msg: {}}}", self.msg) | ||
} | ||
} | ||
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/// Build a bcf or vcf.gz index. | ||
/// Builds tbi or csi depending on index_type. | ||
/// | ||
///``` | ||
/// // Index a sorted bcf file with csi. | ||
/// let bcf_path = concat!(env!("CARGO_MANIFEST_DIR"), "/test/test_multi.bcf"); | ||
/// rust_htslib::bcf::index::build(&bcf_path, Some(&"built_test.csi"), /*n_threads=*/ 4u32, rust_htslib::bcf::index::Type::Csi(14)).expect("Failed to build csi index for bcf file."); | ||
/// assert!(std::path::Path::new(&"built_test.csi").exists()); | ||
/// | ||
/// // Index a bgzip-compresed vcf file with tabix. | ||
/// let vcf_path = concat!(env!("CARGO_MANIFEST_DIR"), "/test/test_left.vcf.gz"); | ||
/// rust_htslib::bcf::index::build(&vcf_path, Some(&"built_test_vcf.tbx"), /*n_threads=*/ 4u32, rust_htslib::bcf::index::Type::Tbx).expect("Failed to build tbx index for vcf file."); | ||
/// assert!(std::path::Path::new(&"built_test_vcf.tbx").exists()); | ||
/// | ||
/// // Cannot build a tbi index for a bcf file: returns an Err(BcfBuildError). | ||
/// assert!(std::panic::catch_unwind(|| rust_htslib::bcf::index::build(bcf_path, Some("built_test.tbi"), 4u32, rust_htslib::bcf::index::Type::Tbx).unwrap()).is_err()); | ||
/// | ||
/// // Cannot built a csi index for a vcf file: returns an Err(BcfBuildError). | ||
/// let vcf_path = concat!(env!("CARGO_MANIFEST_DIR"), "/test/test_various.vcf"); | ||
/// assert!(std::panic::catch_unwind(|| rust_htslib::bcf::index::build(&vcf_path, Some(&"built_test_vcf.csi"), /*n_threads=*/ 4u32, rust_htslib::bcf::index::Type::Csi(14)).expect("Failed to build csi index for vcf file.")).is_err()); | ||
///``` | ||
/// | ||
pub fn build<P: AsRef<std::path::Path>>( | ||
bcf_path: P, | ||
idx_path: Option<P>, | ||
n_threads: u32, | ||
index_type: Type, | ||
) -> Result<(), BcfBuildError> { | ||
let min_shift = index_type.min_shift(); | ||
let idx_path_cstr = idx_path.and_then(|x| utils::path_to_cstring(&x)); | ||
let bcf_path = utils::path_to_cstring(&bcf_path).ok_or(BcfBuildError { | ||
msg: format!( | ||
"Failed to format bcf_path to cstring: {:?}", | ||
bcf_path.as_ref().display() | ||
), | ||
})?; | ||
let return_code = unsafe { | ||
htslib::bcf_index_build3( | ||
bcf_path.as_ptr(), | ||
idx_path_cstr | ||
.as_ref() | ||
.map_or(std::ptr::null(), |p| p.as_ptr()), | ||
min_shift, | ||
n_threads as i32, | ||
) | ||
}; | ||
if return_code == 0 { | ||
Ok(()) | ||
} else { | ||
Err(BcfBuildError { | ||
msg: format!( | ||
"Failed to build bcf index. Error: {return_code:?}/{}", | ||
BcfBuildError::error_message(return_code) | ||
), | ||
}) | ||
} | ||
} |
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