build: update to noodles 0.87

wheretrue · Dec 21, 2024 · d866224 · d866224
1 parent f971daa
commit d866224
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Showing 3 changed files with 40 additions and 27 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -39,7 +39,7 @@ arrow = { version = "53.3.0" }
 async-trait = "0.1.82"
 datafusion = { version = "43", features = ["compression", "parquet"] }
 futures = "0.3"
-noodles = { version = "0.86" }
+noodles = { version = "0.87" }
 object_store = { version = "0.11.0" }
 tokio = { version = "1", features = ["io-util"] }
 tokio-util = { version = "0.7.13", features = ["compat"] }

diff --git a/exon/exon-gff/src/array_builder.rs b/exon/exon-gff/src/array_builder.rs
@@ -23,7 +23,7 @@ use arrow::{
     error::ArrowError,
 };
 use exon_common::ExonArrayBuilder;
-use noodles::gff::Record;
+use noodles::gff::{record::Strand, Record};
 
 pub struct GFFArrayBuilder {
     seqnames: GenericStringBuilder<i32>,
@@ -107,19 +107,21 @@ impl GFFArrayBuilder {
                 6 => {
                     let strand = record.strand()?;
 
-                    if strand.as_ref() == "" || strand.as_ref() == "." {
-                        self.strands.append_null();
-                    } else {
-                        self.strands.append_value(strand);
+                    match strand {
+                        Strand::None | Strand::Unknown => self.strands.append_null(),
+                        Strand::Forward => self.strands.append_value("+"),
+                        Strand::Reverse => self.strands.append_value("-"),
                     }
                 }
                 7 => {
                     let phase = record.phase();
 
                     match phase {
-                        Some(Ok(phase)) => {
-                            self.phases.append_value(phase);
-                        }
+                        Some(Ok(phase)) => match phase {
+                            noodles::gff::record::Phase::Zero => self.phases.append_value("0"),
+                            noodles::gff::record::Phase::One => self.phases.append_value("1"),
+                            noodles::gff::record::Phase::Two => self.phases.append_value("2"),
+                        },
                         Some(Err(e)) => return Err(ArrowError::ExternalError(Box::new(e))),
                         None => self.phases.append_null(),
                     }