cram/io/writer/builder: Rename Builder::build_with_writer to Builder:…

…:build_from_writer

Closes #295.

noodles-cram/CHANGELOG.md

@@ -18,16 +18,19 @@
 
 ### Changed
 
-  * cram/io/writer/builder: Rename `Builder::build_with_path` to
-    `Builder::build_from_path` ([#295]).
+  * cram/io/writer/builder: Rename `Builder::build_with_path` and
+    `Builder::build_with_writer` to `Builder::build_from_path` and
+    `Builder::build_from_writer`, respectively ([#295]).
 
 [#295]: https://github.com/zaeleus/noodles/issues/295
 
 ### Deprecated
 
-  * cram/io/writer/builder: Deprecate `Builder::build_with_path`.
+  * cram/io/writer/builder: Deprecate `Builder::build_with_path` and
+    `Builder::build_with_writer`.
 
-    Use `Builder::build_from_path` instead.
+    Use `Builder::build_from_path` and `Builder::build_from_writer`,
+    respectively, instead.
 
 ## 0.67.0 - 2024-08-04
 

noodles-cram/examples/cram_write.rs

@@ -71,7 +71,7 @@ fn main() -> Result<(), Box<dyn std::error::Error>> {
     let repository = fasta::Repository::new(reference_sequences);
     let mut writer = cram::io::writer::Builder::default()
         .set_reference_sequence_repository(repository)
-        .build_with_writer(stdout);
+        .build_from_writer(stdout);
 
     writer.write_header(&header)?;
 

noodles-cram/examples/cram_write_async.rs

@@ -68,7 +68,7 @@ async fn main() -> Result<(), Box<dyn std::error::Error>> {
     let repository = fasta::Repository::new(reference_sequences);
     let mut writer = cram::r#async::io::writer::Builder::default()
         .set_reference_sequence_repository(repository)
-        .build_with_writer(io::stdout());
+        .build_from_writer(io::stdout());
 
     writer.write_file_definition().await?;
     writer.write_file_header(&header).await?;

noodles-cram/src/async/io/writer.rs

@@ -42,7 +42,7 @@ where
     /// let writer = cram::r#async::io::Writer::new(io::sink());
     /// ```
     pub fn new(inner: W) -> Self {
-        Builder::default().build_with_writer(inner)
+        Builder::default().build_from_writer(inner)
     }
 
     /// Returns a reference to the underlying writer.

noodles-cram/src/async/io/writer/builder.rs

@@ -73,7 +73,7 @@ impl Builder {
     {
         File::create(dst)
             .await
-            .map(|file| self.build_with_writer(file))
+            .map(|file| self.build_from_writer(file))
     }
 
     /// Builds an async CRAM writer from a path.
@@ -92,9 +92,9 @@ impl Builder {
     /// ```
     /// use noodles_cram as cram;
     /// use tokio::io;
-    /// let writer = cram::r#async::io::writer::Builder::default().build_with_writer(io::sink());
+    /// let writer = cram::r#async::io::writer::Builder::default().build_from_writer(io::sink());
     /// ```
-    pub fn build_with_writer<W>(mut self, writer: W) -> Writer<W>
+    pub fn build_from_writer<W>(mut self, writer: W) -> Writer<W>
     where
         W: AsyncWrite + Unpin,
     {
@@ -112,4 +112,13 @@ impl Builder {
             record_counter: 0,
         }
     }
+
+    /// Builds an async CRAM writer from a writer.
+    #[deprecated(since = "0.68.0", note = "Use `Builder::build_from_writer` instead.")]
+    pub fn build_with_writer<W>(self, writer: W) -> Writer<W>
+    where
+        W: AsyncWrite + Unpin,
+    {
+        self.build_from_writer(writer)
+    }
 }

noodles-cram/src/io/writer.rs

@@ -68,7 +68,7 @@ where
     /// let writer = cram::io::Writer::new(Vec::new());
     /// ```
     pub fn new(inner: W) -> Self {
-        Builder::default().build_with_writer(inner)
+        Builder::default().build_from_writer(inner)
     }
 
     /// Returns a reference to the underlying writer.

noodles-cram/src/io/writer/builder.rs

@@ -104,7 +104,7 @@ impl Builder {
     where
         P: AsRef<Path>,
     {
-        File::create(dst).map(|file| self.build_with_writer(file))
+        File::create(dst).map(|file| self.build_from_writer(file))
     }
 
     /// Builds a CRAM writer from a path.
@@ -122,9 +122,9 @@ impl Builder {
     ///
     /// ```
     /// use noodles_cram::io::writer::Builder;
-    /// let writer = Builder::default().build_with_writer(Vec::new());
+    /// let writer = Builder::default().build_from_writer(Vec::new());
     /// ```
-    pub fn build_with_writer<W>(mut self, writer: W) -> Writer<W>
+    pub fn build_from_writer<W>(mut self, writer: W) -> Writer<W>
     where
         W: Write,
     {
@@ -140,6 +140,15 @@ impl Builder {
             record_counter: 0,
         }
     }
+
+    /// Builds a CRAM writer from a writer.
+    #[deprecated(since = "0.68.0", note = "Use `Builder::build_from_writer` instead.")]
+    pub fn build_with_writer<W>(self, writer: W) -> Writer<W>
+    where
+        W: Write,
+    {
+        self.build_from_writer(writer)
+    }
 }
 
 pub fn uses_cram_3_1_codecs(block_content_encoder_map: &BlockContentEncoderMap) -> bool {

noodles-util/src/alignment/async/io/writer/builder.rs

@@ -171,7 +171,7 @@ impl Builder {
                 let inner: Box<dyn AsyncWrite + Unpin> = Box::new(writer);
                 let inner = cram::r#async::io::writer::Builder::default()
                     .set_reference_sequence_repository(self.reference_sequence_repository)
-                    .build_with_writer(inner);
+                    .build_from_writer(inner);
                 Writer::Cram(inner)
             }
             (Format::Cram, Some(CompressionMethod::Bgzf)) => {

noodles-util/src/alignment/io/writer/builder.rs

@@ -172,7 +172,7 @@ impl Builder {
                 cram::io::writer::Builder::default()
                     .set_reference_sequence_repository(self.reference_sequence_repository)
                     .set_block_content_encoder_map(self.block_content_encoder_map)
-                    .build_with_writer(writer),
+                    .build_from_writer(writer),
             ),
             (Format::Cram, Some(CompressionMethod::Bgzf)) => {
                 return Err(io::Error::new(