Skip to content

Commit

Permalink
Merge pull request #91 from jguhlin/Static-CStr's-definitions
Browse files Browse the repository at this point in the history 
Convert static str to static CStr for simpler code
  • Loading branch information
@jguhlin
jguhlin authored Nov 23, 2024
2 parents 419a83a + 7049365 commit d1d80f1
Show file tree
Hide file tree
Showing 2 changed files with 58 additions and 81 deletions.
4 changes: 2 additions & 2 deletions Cargo.toml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ exclude = ["minimappers2", "fakeminimap2", "minimap2-sys"]

[dependencies]
libc = "0.2"
simdutf8 = { version = "0.1", optional = true }
# simdutf8 = { version = "0.1", optional = true }
needletail = { version = "0.6", optional = true, default-features = false}

# Dep for development
Expand All @@ -53,7 +53,7 @@ default = ["map-file"]
sse2only = ["minimap2-sys/sse2only"]
htslib = ['rust-htslib']
simde = ["minimap2-sys/simde"]
map-file = ["needletail", "simdutf8"]
map-file = ["needletail"] #, "simdutf8"]
zlib-ng = ["minimap2-sys/zlib-ng"]
curl = ["rust-htslib/curl"]
static = ["minimap2-sys/static", "rust-htslib/static"]
Expand Down
135 changes: 56 additions & 79 deletions src/lib.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,6 @@
//! assert_eq!(hits.unwrap().len(), 1);
//! ```
use std::borrow::Cow;
use std::cell::RefCell;

use std::ffi::{CStr, CString};
Expand All @@ -58,9 +57,6 @@ use std::os::unix::ffi::OsStrExt;
use libc::c_void;
use minimap2_sys::*;

#[cfg(feature = "map-file")]
use simdutf8::basic::from_utf8;

#[cfg(feature = "map-file")]
use needletail::parse_fastx_file;

Expand All @@ -75,25 +71,25 @@ pub type IdxOpt = mm_idxopt_t;

// TODO: Probably a better way to handle this...
/// C string constants for passing to minimap2
static LRHQAE: &str = "lr:hqae\0";
static LRHQ: &str = "lr:hq\0";
static SPLICE: &str = "splice\0";
static SPLICEHQ: &str = "splice:hq\0";
static ASM: &str = "asm\0";
static ASM5: &str = "asm5\0";
static ASM10: &str = "asm10\0";
static ASM20: &str = "asm20\0";
static SR: &str = "sr\0";
static MAP_PB: &str = "map-pb\0";
static MAP_HIFI: &str = "map-hifi\0";
static MAP_ONT: &str = "map-ont\0";
static AVA_PB: &str = "ava-pb\0";
static AVA_ONT: &str = "ava-ont\0";
static LRHQAE: &CStr = c"lr:hqae";
static LRHQ: &CStr = c"lr:hq";
static SPLICE: &CStr = c"splice";
static SPLICEHQ: &CStr = c"splice:hq";
static ASM: &CStr = c"asm";
static ASM5: &CStr = c"asm5";
static ASM10: &CStr = c"asm10";
static ASM20: &CStr = c"asm20";
static SR: &CStr = c"sr";
static MAP_PB: &CStr = c"map-pb";
static MAP_HIFI: &CStr = c"map-hifi";
static MAP_ONT: &CStr = c"map-ont";
static AVA_PB: &CStr = c"ava-pb";
static AVA_ONT: &CStr = c"ava-ont";

// These aren't listed in the command anymore, but are still available
static SHORT: &str = "short\0";
static MAP10K: &str = "map10k\0";
static CDNA: &str = "cdna\0";
static SHORT: &CStr = c"short";
static MAP10K: &CStr = c"map10k";
static CDNA: &CStr = c"cdna";

/// Strand enum
#[derive(Debug, PartialEq, Eq, Copy, Clone, Default)]
Expand Down Expand Up @@ -135,51 +131,26 @@ pub enum Preset {
}

// Convert to c string for input into minimap2
impl From<Preset> for *const i8 {
fn from(preset: Preset) -> Self {
match preset {
Preset::LrHqae => LRHQAE.as_bytes().as_ptr() as *const i8,
Preset::LrHq => LRHQ.as_bytes().as_ptr() as *const i8,
Preset::Splice => SPLICE.as_bytes().as_ptr() as *const i8,
Preset::SpliceHq => SPLICEHQ.as_bytes().as_ptr() as *const i8,
Preset::Asm => ASM.as_bytes().as_ptr() as *const i8,
Preset::Asm5 => ASM5.as_bytes().as_ptr() as *const i8,
Preset::Asm10 => ASM10.as_bytes().as_ptr() as *const i8,
Preset::Asm20 => ASM20.as_bytes().as_ptr() as *const i8,
Preset::Sr => SR.as_bytes().as_ptr() as *const i8,
Preset::MapPb => MAP_PB.as_bytes().as_ptr() as *const i8,
Preset::MapHifi => MAP_HIFI.as_bytes().as_ptr() as *const i8,
Preset::MapOnt => MAP_ONT.as_bytes().as_ptr() as *const i8,
Preset::AvaPb => AVA_PB.as_bytes().as_ptr() as *const i8,
Preset::AvaOnt => AVA_ONT.as_bytes().as_ptr() as *const i8,
Preset::Short => SHORT.as_bytes().as_ptr() as *const i8,
Preset::Map10k => MAP10K.as_bytes().as_ptr() as *const i8,
Preset::Cdna => CDNA.as_bytes().as_ptr() as *const i8,
}
}
}

// Convert to c string for input into minimap2
impl From<Preset> for *const u8 {
impl From<Preset> for *const libc::c_char {
fn from(preset: Preset) -> Self {
match preset {
Preset::LrHqae => LRHQAE.as_bytes().as_ptr(),
Preset::LrHq => LRHQ.as_bytes().as_ptr(),
Preset::Splice => SPLICE.as_bytes().as_ptr(),
Preset::SpliceHq => SPLICEHQ.as_bytes().as_ptr(),
Preset::Asm => ASM.as_bytes().as_ptr(),
Preset::Asm5 => ASM5.as_bytes().as_ptr(),
Preset::Asm10 => ASM10.as_bytes().as_ptr(),
Preset::Asm20 => ASM20.as_bytes().as_ptr(),
Preset::Sr => SR.as_bytes().as_ptr(),
Preset::MapPb => MAP_PB.as_bytes().as_ptr(),
Preset::MapHifi => MAP_HIFI.as_bytes().as_ptr(),
Preset::MapOnt => MAP_ONT.as_bytes().as_ptr(),
Preset::AvaPb => AVA_PB.as_bytes().as_ptr(),
Preset::AvaOnt => AVA_ONT.as_bytes().as_ptr(),
Preset::Short => SHORT.as_bytes().as_ptr(),
Preset::Map10k => MAP10K.as_bytes().as_ptr(),
Preset::Cdna => CDNA.as_bytes().as_ptr(),
Preset::LrHqae => LRHQAE.as_ptr(),
Preset::LrHq => LRHQ.as_ptr(),
Preset::Splice => SPLICE.as_ptr(),
Preset::SpliceHq => SPLICEHQ.as_ptr(),
Preset::Asm => ASM.as_ptr(),
Preset::Asm5 => ASM5.as_ptr(),
Preset::Asm10 => ASM10.as_ptr(),
Preset::Asm20 => ASM20.as_ptr(),
Preset::Sr => SR.as_ptr(),
Preset::MapPb => MAP_PB.as_ptr(),
Preset::MapHifi => MAP_HIFI.as_ptr(),
Preset::MapOnt => MAP_ONT.as_ptr(),
Preset::AvaPb => AVA_PB.as_ptr(),
Preset::AvaOnt => AVA_ONT.as_ptr(),
Preset::Short => SHORT.as_ptr(),
Preset::Map10k => MAP10K.as_ptr(),
Preset::Cdna => CDNA.as_ptr(),
}
}
}
Expand Down Expand Up @@ -611,6 +582,7 @@ impl Aligner {
}

// Check options
/// Check if the options are valid - Maps to mm_check_opt in minimap2
pub fn check_opts(&self) -> Result<(), &'static str> {
let result = unsafe { mm_check_opt(&self.idxopt, &self.mapopt) };

Expand Down Expand Up @@ -853,7 +825,7 @@ impl Aligner {
return Err("Sequence is empty");
}

let mut qname_cstring = None;
let qname_cstring;

let query_name_cstr: Option<&CStr> = match query_name.as_ref() {
None => None,
Expand Down Expand Up @@ -1249,7 +1221,7 @@ mod tests {
aligner
});

let aligner = jh.join().unwrap();
let _aligner = jh.join().unwrap();
}

#[test]
Expand Down Expand Up @@ -1285,6 +1257,8 @@ mod tests {
let mappings = aligner_handle.map("ACGGTAGAGAGGAAGAAGAAGGAATAGCGGACTTGTGTATTTTATCGTCATTCGTGGTTATCATATAGTTTATTGATTTGAAGACTACGTAAGTAATTTGAGGACTGATTAAAATTTTCTTTTTTAGCTTAGAGTCAATTAAAGAGGGCAAAATTTTCTCAAAAGACCATGGTGCATATGACGATAGCTTTAGTAGTATGGATTGGGCTCTTCTTTCATGGATGTTATTCAGAAGGAGTGATATATCGAGGTGTTTGAAACACCAGCGACACCAGAAGGCTGTGGATGTTAAATCGTAGAACCTATAGACGAGTTCTAAAATATACTTTGGGGTTTTCAGCGATGCAAAA".as_bytes(), false, false, None, None, Some("Sample Query")).unwrap();
assert!(mappings[0].query_len == Some(NonZeroI32::new(350).unwrap()));
});

jh0.join().unwrap();

let aligner_handle = Arc::clone(&aligner);
let jh1 = thread::spawn(move || {
Expand All @@ -1293,6 +1267,9 @@ mod tests {
let mappings = aligner_handle.map("ACGGTAGAGAGGAAGAAGAAGGAATAGCGGACTTGTGTATTTTATCGTCATTCGTGGTTATCATATAGTTTATTGATTTGAAGACTACGTAAGTAATTTGAGGACTGATTAAAATTTTCTTTTTTAGCTTAGAGTCAATTAAAGAGGGCAAAATTTTCTCAAAAGACCATGGTGCATATGACGATAGCTTTAGTAGTATGGATTGGGCTCTTCTTTCATGGATGTTATTCAGAAGGAGTGATATATCGAGGTGTTTGAAACACCAGCGACACCAGAAGGCTGTGGATGTTAAATCGTAGAACCTATAGACGAGTTCTAAAATATACTTTGGGGTTTTCAGCGATGCAAAA".as_bytes(), false, false, None, None, Some("Sample Query")).unwrap();
assert!(mappings[0].query_len == Some(NonZeroI32::new(350).unwrap()));
});

jh1.join().unwrap();

}

#[test]
Expand Down Expand Up @@ -1325,7 +1302,7 @@ mod tests {
"ACGGTAGAGAGGAAGAAGAAGGAATAGCGGACTTGTGTATTTTATCGTCATTCGTGGTTATCATATAGTTTATTGATTTGAAGACTACGTAAGTAATTTGAGGACTGATTAAAATTTTCTTTTTTAGCTTAGAGTCAATTAAAGAGGGCAAAATTTTCTCAAAAGACCATGGTGCATATGACGATAGCTTTAGTAGTATGGATTGGGCTCTTCTTTCATGGATGTTATTCAGAAGGAGTGATATATCGAG",
];

let results = sequences
let _results = sequences
.par_iter()
.map(|seq| {
aligner
Expand All @@ -1352,13 +1329,13 @@ mod tests {

#[test]
fn idxopt() {
let x: IdxOpt = Default::default();
let _x: IdxOpt = Default::default();
}

#[test]
fn mapopt() {
let x: mm_mapopt_t = Default::default();
let y: MapOpt = Default::default();
let _x: mm_mapopt_t = Default::default();
let _y: MapOpt = Default::default();
}

#[test]
Expand All @@ -1371,7 +1348,7 @@ mod tests {
let idx = None;
let idx_reader = None;

let aligner = Aligner {
let _aligner = Aligner {
idxopt,
mapopt,
threads,
Expand All @@ -1383,17 +1360,17 @@ mod tests {

#[test]
fn aligner_builder() {
let result = Aligner::builder();
let _result = Aligner::builder();
}

#[test]
fn aligner_builder_preset() {
let result = Aligner::builder().preset(Preset::LrHq);
let _result = Aligner::builder().preset(Preset::LrHq);
}

#[test]
fn aligner_builder_preset_with_threads() {
let result = Aligner::builder()
let _result = Aligner::builder()
.preset(Preset::LrHq)
.with_index_threads(1);
}
Expand All @@ -1412,15 +1389,15 @@ mod tests {

#[test]
fn create_index() {
let mut aligner = Aligner::builder()
let aligner = Aligner::builder()
.preset(Preset::MapOnt)
.with_index_threads(1);

println!("{}", aligner.idxopt.w);

assert!(aligner.idxopt.w == 10);

aligner = aligner
aligner
.with_index("test_data/test_data.fasta", Some("test.mmi"))
.unwrap();
}
Expand Down Expand Up @@ -1459,7 +1436,7 @@ mod tests {
// Assert the Display impl for strand works
println!("{}", mappings[0].strand);

let mut aligner = aligner.with_cigar();
let aligner = aligner.with_cigar();

aligner
.map(
Expand Down Expand Up @@ -1626,7 +1603,7 @@ mod tests {
true, true, None, None, Some("Sample Query")).unwrap();
assert_eq!(mappings.len(), 1);

let observed = mappings.pop().unwrap();
let _observed = mappings.pop().unwrap();

assert_eq!(
align.cigar,
Expand Down Expand Up @@ -1948,7 +1925,7 @@ mod tests {
sr.mapopt.best_n = 1;
sr.idxopt.k = 7;

let aligner = Aligner {
let _aligner = Aligner {
mapopt: MapOpt {
best_n: 1,
..Aligner::builder().sr().mapopt
Expand Down

0 comments on commit d1d80f1

Please sign in to comment.