fix: use updated chainfile crate to resolve liftover issues (#43)

Author: jsstevenson

rust/Cargo.toml

@@ -8,8 +8,9 @@ name = "agct"
 crate-type = ["cdylib"]
 
 [dependencies]
-chainfile = "0.2.1"
+chainfile = "0.3.0"
 directories = "5.0"
+omics = { version = "0.2.0", features = ["coordinate"] }
 
 [dependencies.pyo3]
 version = "0.20.2"

rust/src/lib.rs

@@ -1,6 +1,6 @@
 //! Provide Rust-based chainfile wrapping classes.
-use chain::core::{Coordinate, Interval, Strand};
 use chainfile as chain;
+use omics::coordinate::{interbase::Coordinate, interval::interbase::Interval, Strand};
 use pyo3::create_exception;
 use pyo3::exceptions::{PyException, PyFileNotFoundError, PyValueError};
 use pyo3::prelude::*;
@@ -40,7 +40,7 @@ impl Converter {
     }
 
     /// Perform liftover
-    pub fn lift(&self, chrom: &str, pos: usize, strand: &str) -> PyResult<Vec<Vec<String>>> {
+    pub fn lift(&self, chrom: &str, pos: u64, strand: &str) -> PyResult<Vec<Vec<String>>> {
         let parsed_strand = if strand == "+" {
             Strand::Positive
         } else if strand == "-" {
@@ -52,8 +52,8 @@ impl Converter {
             )));
         };
         // safe to unwrap coordinates because `pos` is always an int
-        let start = Coordinate::try_new(chrom, pos, parsed_strand.clone()).unwrap();
-        let end = Coordinate::try_new(chrom, pos + 1, parsed_strand.clone()).unwrap();
+        let start = Coordinate::new(chrom, parsed_strand.clone(), pos);
+        let end = Coordinate::new(chrom, parsed_strand.clone(), pos + 1);
 
         let Ok(interval) = Interval::try_new(start, end) else {
             return Err(ChainfileError::new_err(format!(
@@ -63,7 +63,7 @@ impl Converter {
                 pos + 1
             )));
         };
-        if let Some(liftover_result) = self.machine.liftover(&interval) {
+        if let Some(liftover_result) = self.machine.liftover(interval.clone()) {
             Ok(liftover_result
                 .iter()
                 .map(|r| {

tests/data/ucsc-chainfile/chainfile_hg19_to_hg38_.chain

@@ -1,3 +1,14 @@
+chain 24611930 chr1 249250621 + 206072707 206332221 chr1 248956422 - 42687778 42947276 254
+33374	0	21
+6406	0	1
+95162	1	0
+39481	2	0
+4456	0	1
+25212	55	16
+10374	0	1
+1898	0	2
+43093
+
 chain 14633688187 chr7 159138663 + 10000 159128663 chr7 159345973 + 10000 159335973 7
 222484	50000	10034
 183862	17	0

tests/test_liftover.py

@@ -23,6 +23,10 @@ def test_hg19_to_hg38():
     assert len(result) == 1
     assert result[0] == ("chr7", 140753336, Strand.POSITIVE)
 
+    result = converter.convert_coordinate("chr1", 206072707)
+    assert len(result) == 1
+    assert result[0] == ("chr1", 206268644, Strand.NEGATIVE)
+
     # coordinate exceeds bounds
     result = converter.convert_coordinate("chr7", 14040053136)
     assert result == []