Merge pull request #86 from jguhlin/Change-preset-behavior

More docs

src/lib.rs

@@ -352,11 +352,17 @@ impl Aligner {
 
 impl Aligner {
     /// Ergonomic function for Aligner. Sets the minimap2 preset to lr:hq.
+    /// 
+    /// Presets should be called before any other options are set, as they change multiple
+    /// options at once.
     pub fn lrhq(self) -> Self {
         self.preset(Preset::LrHq)
     }
 
     /// Ergonomic function for Aligner. Sets the minimap2 preset to splice
+    /// 
+    /// Presets should be called before any other options are set, as they change multiple
+    /// options at once.
     /// ```
     /// # use minimap2::*;
     /// Aligner::builder().splice();
@@ -366,6 +372,9 @@ impl Aligner {
     }
 
     /// Ergonomic function for Aligner. Sets the minimap2 preset to splice:hq
+    /// 
+    /// Presets should be called before any other options are set, as they change multiple
+    /// options at once.
     /// ```
     /// # use minimap2::*;
     /// Aligner::builder().splice_hq();
@@ -375,6 +384,9 @@ impl Aligner {
     }
 
     /// Ergonomic function for Aligner. Sets the minimap2 preset to Asm
+    /// 
+    /// Presets should be called before any other options are set, as they change multiple
+    /// options at once.
     /// ```
     /// # use minimap2::*;
     /// Aligner::builder().asm();
@@ -384,6 +396,9 @@ impl Aligner {
     }
 
     /// Ergonomic function for Aligner. Sets the minimap2 preset to Asm5
+    /// 
+    /// Presets should be called before any other options are set, as they change multiple
+    /// options at once.
     /// ```
     /// # use minimap2::*;
     /// Aligner::builder().asm5();
@@ -392,6 +407,9 @@ impl Aligner {
         self.preset(Preset::Asm5)
     }
     /// Ergonomic function for Aligner. Sets the minimap2 preset to Asm10
+    ///
+    /// Presets should be called before any other options are set, as they change multiple
+    /// options at once.
     /// ```
     /// # use minimap2::*;
     /// Aligner::builder().asm10();
@@ -400,6 +418,9 @@ impl Aligner {
         self.preset(Preset::Asm10)
     }
     /// Ergonomic function for Aligner. Sets the minimap2 preset to Asm20
+    /// 
+    /// Presets should be called before any other options are set, as they change multiple
+    /// options at once.
     /// ```
     /// # use minimap2::*;
     /// Aligner::builder().asm20();
@@ -409,6 +430,9 @@ impl Aligner {
     }
 
     /// Ergonomic function for Aligner. Sets the minimap2 preset to sr
+    ///
+    /// Presets should be called before any other options are set, as they change multiple
+    /// options at once.
     /// ```
     /// # use minimap2::*;
     /// Aligner::builder().sr();
@@ -418,6 +442,9 @@ impl Aligner {
     }
 
     /// Ergonomic function for Aligner. Sets the minimap2 preset to MapPb
+    /// 
+    /// Presets should be called before any other options are set, as they change multiple
+    /// options at once.
     /// ```
     /// # use minimap2::*;
     /// Aligner::builder().map_pb();
@@ -427,6 +454,9 @@ impl Aligner {
     }
 
     /// Ergonomic function for Aligner. Sets the minimap2 preset to MapHifi
+    /// 
+    /// Presets should be called before any other options are set, as they change multiple
+    /// options at once.
     /// ```
     /// # use minimap2::*;
     /// Aligner::builder().map_hifi();
@@ -436,6 +466,9 @@ impl Aligner {
     }
 
     /// Ergonomic function for Aligner. Sets the minimap2 preset to MapOnt.
+    /// 
+    /// Presets should be called before any other options are set, as they change multiple
+    /// options at once.
     /// ```
     /// # use minimap2::*;
     /// Aligner::builder().map_ont();
@@ -445,6 +478,9 @@ impl Aligner {
     }
 
     /// Ergonomic function for Aligner. Sets the minimap2 preset to AvaPb
+    /// 
+    /// Presets should be called before any other options are set, as they change multiple
+    /// options at once.
     /// ```
     /// # use minimap2::*;
     /// Aligner::builder().ava_pb();
@@ -466,6 +502,9 @@ impl Aligner {
     }
 
     /// Ergonomic function for Aligner. Sets the minimap2 preset to Short
+    /// 
+    /// Presets should be called before any other options are set, as they change multiple
+    /// options at once.
     /// ```
     /// # use minimap2::*;
     /// Aligner::builder().short();
@@ -475,6 +514,9 @@ impl Aligner {
     }
 
     /// Ergonomic function for Aligner. Sets the minimap2 preset to Map10k
+    /// 
+    /// Presets should be called before any other options are set, as they change multiple
+    /// options at once.
     /// ```
     /// # use minimap2::*;
     /// Aligner::builder().map10k();
@@ -484,6 +526,9 @@ impl Aligner {
     }
 
     /// Ergonomic function for Aligner. Sets the minimap2 preset to cdna
+    /// 
+    /// Presets should be called before any other options are set, as they change multiple
+    /// options at once.
     /// ```
     /// # use minimap2::*;
     /// Aligner::builder().cdna();
@@ -493,19 +538,22 @@ impl Aligner {
     }
 
     /// Create an aligner using a preset.
-    pub fn preset(self, preset: Preset) -> Self {
-        let mut idxopt = IdxOpt::default();
-        let mut mapopt = MapOpt::default();
+    /// 
+    /// Presets should be called before any other options are set, as they change multiple
+    /// options at once.
+    pub fn preset(mut self, preset: Preset) -> Self {
+        // let mut idxopt = IdxOpt::default();
+        // let mut mapopt = MapOpt::default();
 
         unsafe {
-            mm_set_opt(&0, &mut idxopt, &mut mapopt);
-            mm_set_opt(preset.into(), &mut idxopt, &mut mapopt)
+            mm_set_opt(&0, &mut self.idxopt, &mut self.mapopt);
+            mm_set_opt(preset.into(), &mut self.idxopt, &mut self.mapopt)
         };
 
         Self {
-            idxopt,
-            mapopt,
-            ..Default::default()
+            idxopt: self.idxopt,
+            mapopt: self.mapopt,
+            ..self
         }
     }