sam/alignment/record/sequence: Add checked split at

zaeleus · Jul 22, 2024 · 610dc9f · 610dc9f
1 parent dca4c90
commit 610dc9f
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Showing 6 changed files with 89 additions and 2 deletions.
diff --git a/noodles-bam/src/record/sequence.rs b/noodles-bam/src/record/sequence.rs
@@ -82,6 +82,21 @@ impl<'a> sam::alignment::record::Sequence for Sequence<'a> {
         self.get(i)
     }
 
+    fn split_at_checked(
+        &self,
+        mid: usize,
+    ) -> Option<(
+        Box<dyn sam::alignment::record::Sequence + '_>,
+        Box<dyn sam::alignment::record::Sequence + '_>,
+    )> {
+        self.split_at_checked(mid).map(|(left, right)| {
+            (
+                Box::new(left) as Box<dyn sam::alignment::record::Sequence + '_>,
+                Box::new(right) as Box<dyn sam::alignment::record::Sequence + '_>,
+            )
+        })
+    }
+
     fn iter(&self) -> Box<dyn Iterator<Item = u8> + '_> {
         Box::new(self.iter())
     }

diff --git a/noodles-bam/src/record/sequence/subsequence.rs b/noodles-bam/src/record/sequence/subsequence.rs
@@ -77,6 +77,21 @@ impl<'a> sam::alignment::record::Sequence for Subsequence<'a> {
         self.get(i)
     }
 
+    fn split_at_checked(
+        &self,
+        mid: usize,
+    ) -> Option<(
+        Box<dyn sam::alignment::record::Sequence + '_>,
+        Box<dyn sam::alignment::record::Sequence + '_>,
+    )> {
+        self.split_at_checked(mid).map(|(left, right)| {
+            (
+                Box::new(left) as Box<dyn sam::alignment::record::Sequence + '_>,
+                Box::new(right) as Box<dyn sam::alignment::record::Sequence + '_>,
+            )
+        })
+    }
+
     fn iter(&self) -> Box<dyn Iterator<Item = u8> + '_> {
         Box::new(self.iter())
     }

diff --git a/noodles-sam/CHANGELOG.md b/noodles-sam/CHANGELOG.md
@@ -5,7 +5,7 @@
 ### Added
 
   * sam/alignment/record/sequence: Add get base by index (`Sequence::get`)
-    ([#283]).
+    ([#283]) and checked split at (`Sequence::split_at_checked`).
 
 [#283]: https://github.com/zaeleus/noodles/issues/283
 

diff --git a/noodles-sam/src/alignment/record/sequence.rs b/noodles-sam/src/alignment/record/sequence.rs
@@ -9,6 +9,12 @@ pub trait Sequence {
     /// Returns the base at the given index.
     fn get(&self, i: usize) -> Option<u8>;
 
+    /// Splits the subsequence into two subsequences at the given index.
+    fn split_at_checked(
+        &self,
+        mid: usize,
+    ) -> Option<(Box<dyn Sequence + '_>, Box<dyn Sequence + '_>)>;
+
     /// Returns an iterator over bases.
     fn iter(&self) -> Box<dyn Iterator<Item = u8> + '_>;
 }
@@ -35,6 +41,13 @@ impl Sequence for Box<dyn Sequence + '_> {
         (**self).get(i)
     }
 
+    fn split_at_checked(
+        &self,
+        mid: usize,
+    ) -> Option<(Box<dyn Sequence + '_>, Box<dyn Sequence + '_>)> {
+        (**self).split_at_checked(mid)
+    }
+
     fn iter(&self) -> Box<dyn Iterator<Item = u8> + '_> {
         (**self).iter()
     }
@@ -61,6 +74,14 @@ mod tests {
                 self.0.get(i).copied()
             }
 
+            fn split_at_checked(
+                &self,
+                mid: usize,
+            ) -> Option<(Box<dyn Sequence + '_>, Box<dyn Sequence + '_>)> {
+                let (left, right) = self.0.split_at(mid);
+                Some((Box::new(T(left.to_vec())), Box::new(T(right.to_vec()))))
+            }
+
             fn iter(&self) -> Box<dyn Iterator<Item = u8> + '_> {
                 Box::new(self.0.iter().copied())
             }

diff --git a/noodles-sam/src/alignment/record_buf/sequence.rs b/noodles-sam/src/alignment/record_buf/sequence.rs
@@ -92,6 +92,24 @@ impl crate::alignment::record::Sequence for &Sequence {
         self.0.get(i).copied()
     }
 
+    fn split_at_checked(
+        &self,
+        mid: usize,
+    ) -> Option<(
+        Box<dyn crate::alignment::record::Sequence + '_>,
+        Box<dyn crate::alignment::record::Sequence + '_>,
+    )> {
+        if mid > self.len() {
+            let (left, right) = self.0.split_at(mid);
+            Some((
+                Box::new(crate::record::Sequence::new(left)),
+                Box::new(crate::record::Sequence::new(right)),
+            ))
+        } else {
+            None
+        }
+    }
+
     fn iter(&self) -> Box<dyn Iterator<Item = u8> + '_> {
         Box::new(self.0.iter().copied())
     }

diff --git a/noodles-sam/src/record/sequence.rs b/noodles-sam/src/record/sequence.rs
@@ -3,7 +3,7 @@
 pub struct Sequence<'a>(&'a [u8]);
 
 impl<'a> Sequence<'a> {
-    pub(super) fn new(buf: &'a [u8]) -> Self {
+    pub(crate) fn new(buf: &'a [u8]) -> Self {
         Self(buf)
     }
 
@@ -42,6 +42,24 @@ impl<'a> crate::alignment::record::Sequence for Sequence<'a> {
         self.get(i)
     }
 
+    fn split_at_checked(
+        &self,
+        mid: usize,
+    ) -> Option<(
+        Box<dyn crate::alignment::record::Sequence + '_>,
+        Box<dyn crate::alignment::record::Sequence + '_>,
+    )> {
+        if mid <= self.len() {
+            let (left, right) = self.0.split_at(mid);
+            Some((
+                Box::new(Sequence::new(left)),
+                Box::new(Sequence::new(right)),
+            ))
+        } else {
+            None
+        }
+    }
+
     fn iter(&self) -> Box<dyn Iterator<Item = u8> + '_> {
         Box::new(self.as_ref().iter().copied())
     }