feat: add flag set/unset method

minimap2-sys/Cargo.toml

@@ -34,6 +34,7 @@ crate-type = ["staticlib", "cdylib", "rlib"]
 
 [dependencies]
 libz-sys = { version = "1.1", default-features = false, features = ["libc"] }
+paste = "1.0.15"
 
 [build-dependencies]
 pkg-config = "0.3"

minimap2-sys/src/lib.rs

@@ -14,6 +14,8 @@ unsafe impl Send for mm_idx_t {}
 unsafe impl Send for mm_idx_reader_t {}
 unsafe impl Send for mm_mapopt_t {}
 
+use paste::paste;
+
 impl Drop for mm_idx_t {
     fn drop(&mut self) {
         unsafe { mm_idx_destroy(self) };
@@ -60,6 +62,80 @@ impl Default for mm_mapopt_t {
     }
 }
 
+
+macro_rules! add_flag_methods {
+    ($ty:ty, $struct_name:ident, $(($set_name:ident, $unset_name:ident, $flag:expr)),+) => {
+        impl $struct_name {
+            $(
+                paste! {
+                    #[inline(always)]
+                    #[doc = "Set the " $flag " flag"]
+                    pub fn $set_name(&mut self) {
+                        self.flag |= $flag as $ty;
+                    }
+
+                    #[inline(always)]
+                    #[doc = "Unset the " $flag " flag"]
+                    pub fn $unset_name(&mut self) {
+                        self.flag &= !$flag as $ty;
+                    }
+                }
+            )*
+        }
+    };
+}
+
+add_flag_methods!(
+    i64,
+    mm_mapopt_t,
+    (set_no_dual, unset_no_dual, MM_F_NO_DUAL),
+    (set_no_diag, unset_no_diag, MM_F_NO_DIAG),
+    (set_cigar, unset_cigar, MM_F_CIGAR),
+    (set_out_sam, unset_out_sam, MM_F_OUT_SAM),
+    (set_no_qual, unset_no_qual, MM_F_NO_QUAL),
+    (set_out_cg, unset_out_cg, MM_F_OUT_CG),
+    (set_out_cs, unset_out_cs, MM_F_OUT_CS),
+    (set_splice, unset_splice, MM_F_SPLICE),
+    (set_splice_for, unset_splice_for, MM_F_SPLICE_FOR),
+    (set_splice_rev, unset_splice_rev, MM_F_SPLICE_REV),
+    (set_no_ljoin, unset_no_ljoin, MM_F_NO_LJOIN),
+    (set_out_cs_long, unset_out_cs_long, MM_F_OUT_CS_LONG),
+    (set_sr, unset_sr, MM_F_SR),
+    (set_frag_mode, unset_frag_mode, MM_F_FRAG_MODE),
+    (set_no_print_2nd, unset_no_print_2nd, MM_F_NO_PRINT_2ND),
+    (set_two_io_threads, unset_two_io_threads, MM_F_2_IO_THREADS),
+    (set_long_cigar, unset_long_cigar, MM_F_LONG_CIGAR),
+    (set_indep_seg, unset_indep_seg, MM_F_INDEPEND_SEG),
+    (set_splice_flank, unset_splice_flank, MM_F_SPLICE_FLANK),
+    (set_softclip, unset_softclip, MM_F_SOFTCLIP),
+    (set_for_only, unset_for_only, MM_F_FOR_ONLY),
+    (set_rev_only, unset_rev_only, MM_F_REV_ONLY),
+    (set_heap_sort, unset_heap_sort, MM_F_HEAP_SORT),
+    (set_all_chains, unset_all_chains, MM_F_ALL_CHAINS),
+    (set_out_md, unset_out_md, MM_F_OUT_MD),
+    (set_copy_comment, unset_copy_comment, MM_F_COPY_COMMENT),
+    (set_eqx, unset_eqx, MM_F_EQX),
+    (set_paf_no_hit, unset_paf_no_hit, MM_F_PAF_NO_HIT),
+    (set_no_end_flt, unset_no_end_flt, MM_F_NO_END_FLT),
+    (set_hard_mlevel, unset_hard_mlevel, MM_F_HARD_MLEVEL),
+    (set_sam_hit_only, unset_sam_hit_only, MM_F_SAM_HIT_ONLY),
+    (set_rmq, unset_rmq, MM_F_RMQ),
+    (set_qstrand, unset_qstrand, MM_F_QSTRAND),
+    (set_no_inv, unset_no_inv, MM_F_NO_INV),
+    (set_no_hash_name, unset_no_hash_name, MM_F_NO_HASH_NAME),
+    (set_splice_old, unset_splice_old, MM_F_SPLICE_OLD),
+    (set_secondary_seq, unset_secondary_seq, MM_F_SECONDARY_SEQ),
+    (set_out_ds, unset_out_ds, MM_F_OUT_DS)
+);
+
+add_flag_methods!(
+    std::os::raw::c_short,
+    mm_idxopt_t,
+    (set_hpc, unset_hpc, MM_I_HPC),
+    (set_no_seq, unset_no_seq, MM_I_NO_SEQ),
+    (set_no_name, unset_no_name, MM_I_NO_NAME)
+);
+
 impl Default for mm_idxopt_t {
     fn default() -> Self {
         unsafe {
@@ -101,4 +177,24 @@ mod tests {
     fn idxopt() {
         let x: mm_idxopt_t = Default::default();
     }
+
+    #[test]
+    fn test_mapopt_flags() {
+        let mut opt = mm_mapopt_t::default();
+        opt.set_no_qual();
+        assert_eq!(opt.flag & MM_F_NO_QUAL as i64, MM_F_NO_QUAL as i64);
+
+        opt.unset_no_qual();
+        assert_eq!(opt.flag & MM_F_NO_QUAL as i64, 0_i64);
+    }
+
+    #[test]
+    fn test_idxopt_flags() {
+        let mut opt = mm_idxopt_t::default();
+        opt.set_hpc();
+        assert_eq!(opt.flag & MM_I_HPC as i16, MM_I_HPC as i16);
+
+        opt.unset_hpc();
+        assert_eq!(opt.flag & MM_I_HPC as i16, 0_i16);
+    }
 }

src/lib.rs

@@ -1498,6 +1498,27 @@ mod tests {
         };
     }
 
+    #[test]
+    fn test_mapopt_flags_in_aligner() {
+        let mut aligner = Aligner::builder();
+        aligner.mapopt.set_no_qual();
+        assert_eq!(
+            aligner.mapopt.flag & MM_F_NO_QUAL as i64,
+            MM_F_NO_QUAL as i64
+        );
+        aligner.mapopt.unset_no_qual();
+        assert_eq!(aligner.mapopt.flag & MM_F_NO_QUAL as i64, 0_i64);
+    }
+
+    #[test]
+    fn test_idxopt_flags_in_aligner() {
+        let mut aligner = Aligner::builder();
+        aligner.idxopt.set_hpc();
+        assert_eq!(aligner.idxopt.flag & MM_I_HPC as i16, MM_I_HPC as i16);
+        aligner.idxopt.unset_hpc();
+        assert_eq!(aligner.idxopt.flag & MM_I_HPC as i16, 0_i16);
+    }
+
     #[test]
     fn aligner_builder() {
         let _result = Aligner::builder();