Add astarpa2::astarpa2_{simple,full} to C api and example

README.org

@@ -62,7 +62,7 @@ More complex usage examples can be found in [[file:pa-bin/examples/][pa-bin/exam
 
 ** C API
 The ~astarpa-c~ [[file:astarpa-c/astarpa.h][crate]] contains simple C-bindings for the
-~astarpa::{astarpa,astarpa_gcsh}~ functions and an [[file:astarpa-c/example.c][example]] with [[file:astarpa-c/makefile][makefile]]. More should not be needed for
+~astarpa::{astarpa,astarpa_gcsh}~ and ~astarpa2::astarpa2_{simple,full}~ functions and an [[file:astarpa-c/example.c][example]] with [[file:astarpa-c/makefile][makefile]]. More should not be needed for
 simple usage. To run the resulting binary, make sure to ~export
 LD_LIBRARY_PATH=/path/to/astarpa/target/release~.
 

astarpa-c/Cargo.toml

@@ -10,3 +10,4 @@ crate-type = ["lib", "cdylib", "staticlib"]
 astarpa.workspace = true
 pa-types.workspace = true
 pa-heuristic.workspace = true
+astarpa2.workspace = true

astarpa-c/astarpa.h

@@ -7,6 +7,30 @@
 extern "C" {
 #endif // __cplusplus
 
+/**
+ * Align sequences `a` and `b` of length `a_len` and `b_len` using A*PA2-simple.
+ *
+ * The returned cigar must be freed using `astarpa_free_cigar`.
+ */
+uint64_t astarpa2_simple(const uint8_t *a,
+                         uintptr_t a_len,
+                         const uint8_t *b,
+                         uintptr_t b_len,
+                         uint8_t **cigar_ptr,
+                         uintptr_t *cigar_len);
+
+/**
+ * Align sequences `a` and `b` of length `a_len` and `b_len` using A*PA2-full.
+ *
+ * The returned cigar must be freed using `astarpa_free_cigar`.
+ */
+uint64_t astarpa2_full(const uint8_t *a,
+                       uintptr_t a_len,
+                       const uint8_t *b,
+                       uintptr_t b_len,
+                       uint8_t **cigar_ptr,
+                       uintptr_t *cigar_len);
+
 /**
  * Globally align sequences `a` and `b` of length `a_len` and `b_len`.
  * This uses A*PA with GCSH with DT, inexact matches (r=2), seed length k=15, and pruning by start of matches.

astarpa-c/example.c

@@ -9,8 +9,23 @@ int main() {
 	const char* b = "AACTCGTT";
 	size_t len;
 	uint8_t* cigar;
-	uint64_t cost =
-	    astarpa((const uint8_t*)a, strlen(a), (const uint8_t*)b, strlen(b), &cigar, &len);
+	uint64_t cost;
+
+	cost = astarpa((const uint8_t*)a, strlen(a), (const uint8_t*)b, strlen(b), &cigar, &len);
+	assert(cost == 2);
+	astarpa_free_cigar(cigar);
+
+	cost = astarpa_gcsh((const uint8_t*)a, strlen(a), (const uint8_t*)b, strlen(b), 1, 15, false,
+	                    &cigar, &len);
+	assert(cost == 2);
+	astarpa_free_cigar(cigar);
+
+	cost =
+	    astarpa2_simple((const uint8_t*)a, strlen(a), (const uint8_t*)b, strlen(b), &cigar, &len);
+	assert(cost == 2);
+	astarpa_free_cigar(cigar);
+
+	cost = astarpa2_full((const uint8_t*)a, strlen(a), (const uint8_t*)b, strlen(b), &cigar, &len);
 	assert(cost == 2);
 	printf("Cost: %lu\n", cost);
 	printf("Cigar len: %lu\n", len);

astarpa-c/src/lib.rs

@@ -1,6 +1,50 @@
 use pa_heuristic::Prune;
 use std::ffi::CString;
 
+/// Align sequences `a` and `b` of length `a_len` and `b_len` using A*PA2-simple.
+///
+/// The returned cigar must be freed using `astarpa_free_cigar`.
+#[no_mangle]
+pub unsafe extern "C" fn astarpa2_simple(
+    a: *const u8,
+    a_len: usize,
+    b: *const u8,
+    b_len: usize,
+    // output parameters
+    cigar_ptr: *mut *mut u8,
+    cigar_len: *mut usize,
+) -> u64 {
+    let a = std::slice::from_raw_parts(a, a_len);
+    let b = std::slice::from_raw_parts(b, b_len);
+    let (cost, cigar) = astarpa2::astarpa2_simple(a, b);
+    let cigar_string = cigar.to_string();
+    *cigar_len = cigar_string.len();
+    *cigar_ptr = CString::new(cigar_string).unwrap().into_raw() as *mut u8;
+    cost as _
+}
+
+/// Align sequences `a` and `b` of length `a_len` and `b_len` using A*PA2-full.
+///
+/// The returned cigar must be freed using `astarpa_free_cigar`.
+#[no_mangle]
+pub unsafe extern "C" fn astarpa2_full(
+    a: *const u8,
+    a_len: usize,
+    b: *const u8,
+    b_len: usize,
+    // output parameters
+    cigar_ptr: *mut *mut u8,
+    cigar_len: *mut usize,
+) -> u64 {
+    let a = std::slice::from_raw_parts(a, a_len);
+    let b = std::slice::from_raw_parts(b, b_len);
+    let (cost, cigar) = astarpa2::astarpa2_full(a, b);
+    let cigar_string = cigar.to_string();
+    *cigar_len = cigar_string.len();
+    *cigar_ptr = CString::new(cigar_string).unwrap().into_raw() as *mut u8;
+    cost as _
+}
+
 /// Globally align sequences `a` and `b` of length `a_len` and `b_len`.
 /// This uses A*PA with GCSH with DT, inexact matches (r=2), seed length k=15, and pruning by start of matches.
 ///