vcf/variant/io/read: Change Read::variant_records to return an iterat…

…or over Record trait objects
zaeleus · Mar 18, 2024 · fc124c4 · fc124c4
1 parent 20cf3e9
commit fc124c4
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Showing 7 changed files with 23 additions and 12 deletions.
diff --git a/noodles-bcf/src/io/reader.rs b/noodles-bcf/src/io/reader.rs
@@ -338,9 +338,13 @@ where
 
     fn variant_records<'r, 'h: 'r>(
         &'r mut self,
-        header: &'h vcf::Header,
-    ) -> Box<dyn Iterator<Item = io::Result<RecordBuf>> + 'r> {
-        Box::new(self.record_bufs(header))
+        _: &'h vcf::Header,
+    ) -> Box<dyn Iterator<Item = io::Result<Box<dyn vcf::variant::Record>>> + 'r> {
+        Box::new(
+            self.records().map(|result| {
+                result.map(|record| Box::new(record) as Box<dyn vcf::variant::Record>)
+            }),
+        )
     }
 }
 

diff --git a/noodles-util/CHANGELOG.md b/noodles-util/CHANGELOG.md
@@ -7,6 +7,9 @@
   * util/variant: Move readers (`Reader` and `IndexedReader`) and writer
     (`Writer`) to `io` module.
 
+  * util/variant/io/reader: Change `Reader::records` to return an iterator
+    over `vcf::variant::Record` trait objects.
+
   * util/variant/io/writer: Change `Writer::write_record` to accept `&dyn
     vcf::variant::Record`.
 

diff --git a/noodles-util/examples/util_variant_rewrite.rs b/noodles-util/examples/util_variant_rewrite.rs
@@ -22,7 +22,7 @@ fn main() -> io::Result<()> {
 
     for result in reader.records(&header) {
         let record = result?;
-        writer.write_record(&header, &record)?;
+        writer.write_record(&header, record.as_ref())?;
     }
 
     Ok(())

diff --git a/noodles-util/examples/util_variant_view.rs b/noodles-util/examples/util_variant_view.rs
@@ -31,7 +31,7 @@ fn main() -> io::Result<()> {
 
     for result in reader.records(&header) {
         let record = result?;
-        writer.write_variant_record(&header, &record)?;
+        writer.write_variant_record(&header, record.as_ref())?;
     }
 
     Ok(())

diff --git a/noodles-util/src/variant/io/reader.rs b/noodles-util/src/variant/io/reader.rs
@@ -6,7 +6,7 @@ pub use self::builder::Builder;
 
 use std::io::{self, BufRead};
 
-use noodles_vcf::{self as vcf, variant::RecordBuf};
+use noodles_vcf::{self as vcf, variant::Record};
 
 /// A variant reader.
 pub struct Reader<R> {
@@ -69,7 +69,7 @@ where
     pub fn records<'a>(
         &'a mut self,
         header: &'a vcf::Header,
-    ) -> impl Iterator<Item = io::Result<RecordBuf>> + 'a {
+    ) -> impl Iterator<Item = io::Result<Box<dyn Record>>> + 'a {
         self.inner.variant_records(header)
     }
 }
diff --git a/noodles-vcf/src/io/reader.rs b/noodles-vcf/src/io/reader.rs
@@ -396,9 +396,13 @@ where
 
     fn variant_records<'r, 'h: 'r>(
         &'r mut self,
-        header: &'h Header,
-    ) -> Box<dyn Iterator<Item = io::Result<RecordBuf>> + 'r> {
-        Box::new(self.record_bufs(header))
+        _: &'h Header,
+    ) -> Box<dyn Iterator<Item = io::Result<Box<dyn crate::variant::Record>>> + 'r> {
+        Box::new(
+            self.records().map(|result| {
+                result.map(|record| Box::new(record) as Box<dyn crate::variant::Record>)
+            }),
+        )
     }
 }
 

diff --git a/noodles-vcf/src/variant/io/read.rs b/noodles-vcf/src/variant/io/read.rs
@@ -1,6 +1,6 @@
 use std::io;
 
-use crate::{variant::RecordBuf, Header};
+use crate::{variant::Record, Header};
 
 /// A variant format reader.
 pub trait Read<R> {
@@ -11,5 +11,5 @@ pub trait Read<R> {
     fn variant_records<'r, 'h: 'r>(
         &'r mut self,
         header: &'h Header,
-    ) -> Box<dyn Iterator<Item = io::Result<RecordBuf>> + 'r>;
+    ) -> Box<dyn Iterator<Item = io::Result<Box<dyn Record>>> + 'r>;
 }