vcf/variant/record_buf/info/field: Move key to record

zaeleus · Mar 13, 2024 · ccc8141 · ccc8141
1 parent c48ff83
commit ccc8141
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Showing 22 changed files with 71 additions and 67 deletions.
diff --git a/noodles-bcf/src/async/io/reader/record.rs b/noodles-bcf/src/async/io/reader/record.rs
@@ -34,9 +34,11 @@ mod tests {
     use noodles_vcf::{
         self as vcf,
         variant::{
-            record::{info::field::Value as InfoFieldValue, AlternateBases, Filters, Info},
+            record::{
+                info::{self, field::Value as InfoFieldValue},
+                AlternateBases, Filters, Info,
+            },
             record_buf::{
-                info,
                 samples::{self, sample::Value as GenotypeFieldValue, Keys},
                 Samples as VcfGenotypes,
             },

diff --git a/noodles-bcf/src/io/reader/record.rs b/noodles-bcf/src/io/reader/record.rs
@@ -108,9 +108,9 @@ pub(crate) mod tests {
         use noodles_vcf::{
             self as vcf,
             variant::{
-                record::{AlternateBases, Filters, Info},
+                record::{info, AlternateBases, Filters, Info},
                 record_buf::{
-                    info::{self, field::Value as InfoFieldValue},
+                    info::field::Value as InfoFieldValue,
                     samples::{
                         self,
                         sample::{value::Array, Value as GenotypeFieldValue},

diff --git a/noodles-vcf/src/header.rs b/noodles-vcf/src/header.rs
@@ -116,7 +116,7 @@ impl Header {
     /// use noodles_vcf::{
     ///     self as vcf,
     ///     header::record::value::{map::Info, Map},
-    ///     variant::record_buf::info::field::key,
+    ///     variant::record::info::field::key,
     /// };
     ///
     /// let id = key::SAMPLES_WITH_DATA_COUNT;
@@ -142,7 +142,7 @@ impl Header {
     /// use noodles_vcf::{
     ///     self as vcf,
     ///     header::record::value::{map::Info, Map},
-    ///     variant::record_buf::info::field::key,
+    ///     variant::record::info::field::key,
     /// };
     ///
     /// let mut header = vcf::Header::default();

diff --git a/noodles-vcf/src/header/builder.rs b/noodles-vcf/src/header/builder.rs
@@ -52,7 +52,7 @@ impl Builder {
     /// use noodles_vcf::{
     ///     self as vcf,
     ///     header::record::value::{map::Info, Map},
-    ///     variant::record_buf::info::field::key,
+    ///     variant::record::info::field::key,
     /// };
     ///
     /// let id = key::SAMPLES_WITH_DATA_COUNT;
@@ -322,7 +322,9 @@ mod tests {
     fn test_build() -> Result<(), Box<dyn std::error::Error>> {
         use crate::{
             header,
-            variant::record_buf::{info::field::key as info_key, samples::keys::key as format_key},
+            variant::{
+                record::info::field::key as info_key, record_buf::samples::keys::key as format_key,
+            },
         };
 
         let (key, value) = (

diff --git a/noodles-vcf/src/header/parser.rs b/noodles-vcf/src/header/parser.rs
@@ -419,7 +419,8 @@ mod tests {
     fn test_from_str() -> Result<(), Box<dyn std::error::Error>> {
         use crate::{
             header::record::{value::map::Other, Value},
-            variant::record_buf::{info, samples},
+            variant::record::info,
+            variant::record_buf::samples,
         };
 
         let s = r#"##fileformat=VCFv4.3

diff --git a/noodles-vcf/src/header/parser/record/value/map/info.rs b/noodles-vcf/src/header/parser/record/value/map/info.rs
@@ -190,7 +190,7 @@ fn try_insert(
 #[cfg(test)]
 mod tests {
     use super::*;
-    use crate::variant::record_buf::info::field::key;
+    use crate::variant::record::info::field::key;
 
     #[test]
     fn test_parse_info() {

diff --git a/noodles-vcf/src/header/record/value/map/info.rs b/noodles-vcf/src/header/record/value/map/info.rs
@@ -71,7 +71,7 @@ impl Map<Info> {
     /// ```
     /// use noodles_vcf::{
     ///     header::{record::value::{map::{info::Type, Info}, Map}, Number},
-    ///     variant::record_buf::info::field::key,
+    ///     variant::record::info::field::key,
     /// };
     ///
     /// let id = key::SAMPLES_WITH_DATA_COUNT;

diff --git a/noodles-vcf/src/header/record/value/map/info/definition/v4_3.rs b/noodles-vcf/src/header/record/value/map/info/definition/v4_3.rs
@@ -1,6 +1,6 @@
 use crate::{
     header::{record::value::map::info::Type, Number},
-    variant::record_buf::info::field::key,
+    variant::record::info::field::key,
 };
 
 pub(super) fn definition(key: &str) -> Option<(Number, Type, &'static str)> {

diff --git a/noodles-vcf/src/header/record/value/map/info/definition/v4_4.rs b/noodles-vcf/src/header/record/value/map/info/definition/v4_4.rs
@@ -1,6 +1,6 @@
 use crate::{
     header::{record::value::map::info::Type, Number},
-    variant::record_buf::info::field::key,
+    variant::record::info::field::key,
 };
 
 pub(super) fn definition(key: &str) -> Option<(Number, Type, &'static str)> {

diff --git a/noodles-vcf/src/header/string_maps.rs b/noodles-vcf/src/header/string_maps.rs
@@ -42,7 +42,7 @@ impl StringMaps {
     ///         record::value::{map::{Contig, Filter, Format, Info}, Map},
     ///         StringMaps,
     ///     },
-    ///     variant::record_buf::{info, samples},
+    ///     variant::{record::info, record_buf::samples},
     /// };
     ///
     /// let header = vcf::Header::builder()
@@ -80,7 +80,7 @@ impl StringMaps {
     ///         record::value::{map::{Contig, Filter, Format, Info}, Map},
     ///         StringMaps,
     ///     },
-    ///     variant::record_buf::{info, samples},
+    ///     variant::{record::info, record_buf::samples},
     /// };
     ///
     /// let header = vcf::Header::builder()
@@ -412,7 +412,8 @@ mod tests {
                 map::{AlternativeAllele, Contig, Filter, Format, Info},
                 Map,
             },
-            variant::record_buf::{info, samples},
+            variant::record::info,
+            variant::record_buf::samples,
         };
 
         let header = Header::builder()
@@ -494,7 +495,7 @@ mod tests {
                 map::{Filter, Info},
                 Map,
             },
-            variant::record_buf::info,
+            variant::record::info,
         };
 
         let ns = {

diff --git a/noodles-vcf/src/io/reader/record_buf/info.rs b/noodles-vcf/src/io/reader/record_buf/info.rs
@@ -75,7 +75,7 @@ mod tests {
 
     #[test]
     fn test_parse_info() -> Result<(), ParseError> {
-        use crate::variant::record_buf::info::field::{key, Value};
+        use crate::variant::{record::info::field::key, record_buf::info::field::Value};
 
         let header = Header::default();
         let mut info = Info::default();

diff --git a/noodles-vcf/src/io/reader/record_buf/info/field.rs b/noodles-vcf/src/io/reader/record_buf/info/field.rs
@@ -99,7 +99,7 @@ pub(super) fn parse_field(header: &Header, s: &str) -> Result<(String, Option<Va
 #[cfg(test)]
 mod tests {
     use super::*;
-    use crate::variant::record_buf::info::field::key;
+    use crate::variant::record::info::field::key;
 
     #[test]
     fn test_parse_field() {

diff --git a/noodles-vcf/src/io/writer/header/record/value/map/info.rs b/noodles-vcf/src/io/writer/header/record/value/map/info.rs
@@ -17,7 +17,7 @@ where
 #[cfg(test)]
 mod tests {
     use super::*;
-    use crate::variant::record_buf::info::field::key;
+    use crate::variant::record::info::field::key;
 
     #[test]
     fn test_write_info() -> Result<(), Box<dyn std::error::Error>> {

diff --git a/noodles-vcf/src/io/writer/record/info.rs b/noodles-vcf/src/io/writer/record/info.rs
@@ -127,9 +127,9 @@ mod tests {
 
     #[test]
     fn test_write_info() -> io::Result<()> {
-        use crate::variant::record_buf::{
-            info::field::{key, Value as ValueBuf},
-            Info as InfoBuf,
+        use crate::variant::{
+            record::info::field::key,
+            record_buf::{info::field::Value as ValueBuf, Info as InfoBuf},
         };
 
         fn t(

diff --git a/noodles-vcf/src/record/info.rs b/noodles-vcf/src/record/info.rs
@@ -108,7 +108,7 @@ mod tests {
 
     #[test]
     fn test_iter() {
-        use crate::variant::record_buf::info::field::key;
+        use crate::variant::record::info::field::key;
 
         let header = Header::default();
 

diff --git a/noodles-vcf/src/variant/record.rs b/noodles-vcf/src/variant/record.rs
@@ -48,8 +48,7 @@ pub trait Record {
 
     /// Returns or calculates the end.
     fn end(&self, header: &Header) -> io::Result<Position> {
-        use self::info::field::Value;
-        use super::record_buf::info::field::key;
+        use self::info::field::{key, Value};
 
         if let Some(Some(value)) = self.info().get(header, key::END_POSITION).transpose()? {
             match value {
@@ -90,10 +89,7 @@ mod tests {
 
     #[test]
     fn test_end() -> Result<(), Box<dyn std::error::Error>> {
-        use crate::variant::{
-            record_buf::info::field::{key, Value},
-            RecordBuf,
-        };
+        use crate::variant::{record::info::field::key, record_buf::info::field::Value, RecordBuf};
 
         let header = Header::default();
 

diff --git a/noodles-vcf/src/variant/record/info/field.rs b/noodles-vcf/src/variant/record/info/field.rs
@@ -1,5 +1,6 @@
 //! Variant record info field.
 
+pub mod key;
 pub mod value;
 
 pub use self::value::Value;
diff --git a/.../src/variant/record_buf/info/field/key.rs → ...-vcf/src/variant/record/info/field/key.rs b/.../src/variant/record_buf/info/field/key.rs → ...-vcf/src/variant/record/info/field/key.rs
diff --git a/noodles-vcf/src/variant/record_buf.rs b/noodles-vcf/src/variant/record_buf.rs
@@ -317,9 +317,9 @@ impl RecordBuf {
     /// ```
     /// use noodles_vcf::{
     ///     self as vcf,
-    ///     variant::record_buf::{
-    ///         info::field::{key, Value},
-    ///         Info,
+    ///     variant::{
+    ///         record::info::field::key,
+    ///         record_buf::{info::field::Value, Info},
     ///     },
     /// };
     ///
@@ -347,10 +347,10 @@ impl RecordBuf {
     /// ```
     /// use noodles_vcf::{
     ///     self as vcf,
-    ///     variant::record_buf::{
-    ///         info::field::{key, Value},
-    ///         Info,
-    ///     },
+    ///     variant::{
+    ///         record::info::field::key,
+    ///         record_buf::{info::field::Value, Info},
+    ///     }
     /// };
     ///
     /// let info: Info = [
@@ -556,7 +556,7 @@ impl RecordBuf {
     /// use noodles_core::Position;
     /// use noodles_vcf::{
     ///     self as vcf,
-    ///     variant::record_buf::info::field::{key, Value},
+    ///     variant::{record::info::field::key, record_buf::info::field::Value},
     /// };
     ///
     /// let record = vcf::variant::RecordBuf::builder()
@@ -590,7 +590,8 @@ impl RecordBuf {
     /// # Ok::<_, noodles_core::position::TryFromIntError>(())
     /// ```
     pub fn end(&self) -> Result<Position, EndError> {
-        use self::info::field::{key, Value};
+        use self::info::field::Value;
+        use super::record::info::field::key;
 
         if let Some(Some(value)) = self.info().get(key::END_POSITION) {
             match value {
@@ -675,7 +676,7 @@ mod tests {
 
     #[test]
     fn test_end() -> Result<(), Box<dyn std::error::Error>> {
-        use super::info::field::key;
+        use crate::variant::record::info::field::key;
 
         let record = RecordBuf::builder()
             .set_reference_sequence_name("sq0")

diff --git a/noodles-vcf/src/variant/record_buf/builder.rs b/noodles-vcf/src/variant/record_buf/builder.rs
@@ -163,9 +163,9 @@ impl Builder {
     /// ```
     /// use noodles_vcf::{
     ///     self as vcf,
-    ///     variant::record_buf::{
-    ///         info::field::{key, Value},
-    ///         Info,
+    ///     variant::{
+    ///         record::info::field::key,
+    ///         record_buf::{info::field::Value, Info},
     ///     },
     /// };
     ///