build: bump noodles (#444)

wheretrue · Mar 17, 2024 · d0499b1 · d0499b1
1 parent ea81d34
commit d0499b1
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Showing 7 changed files with 34 additions and 30 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -38,7 +38,7 @@ arrow = { version = "50.0.0" }
 async-trait = "0.1.77"
 datafusion = { version = "36", features = ["compression", "parquet"] }
 futures = "0.3"
-noodles = { version = "0.65" }
+noodles = { version = "0.66" }
 object_store = { version = "0.9" }
 tokio = { version = "1", features = ["io-util"] }
 tokio-util = { version = "0.7.10", features = ["compat"] }

diff --git a/exon/exon-bam/Cargo.toml b/exon/exon-bam/Cargo.toml
@@ -21,6 +21,6 @@ noodles = { workspace = true, features = [
   "sam",
   "bgzf",
 ] }
-noodles-bgzf = { version = "0.26.0", features = ["libdeflate"] }
+noodles-bgzf = { version = "0.27.0", features = ["libdeflate"] }
 object_store = { workspace = true }
 tokio = { workspace = true }
diff --git a/exon/exon-core/Cargo.toml b/exon/exon-core/Cargo.toml
@@ -42,7 +42,7 @@ noodles = { workspace = true, features = [
   "csi",
   "gtf",
 ] }
-noodles-bgzf = { version = "0.26.0", features = ["libdeflate"] }
+noodles-bgzf = { version = "0.27.0", features = ["libdeflate"] }
 num_cpus = "1.16.0"
 object_store = { workspace = true, features = ["aws"] }
 pin-project = { version = "1.1.5", optional = true }

diff --git a/exon/exon-core/src/udfs/sam/samflags.rs b/exon/exon-core/src/udfs/sam/samflags.rs
@@ -111,7 +111,11 @@ impl ScalarUDFImpl for SAMScalarUDF {
 pub fn register_udfs(ctx: &SessionContext) {
     let udfs = vec![
         SAMScalarUDF::new(Flags::SEGMENTED, "is_segmented".to_string()),
-        SAMScalarUDF::new(Flags::PROPERLY_ALIGNED, "is_properly_aligned".to_string()),
+        SAMScalarUDF::new(Flags::PROPERLY_SEGMENTED, "is_properly_aligned".to_string()),
+        SAMScalarUDF::new(
+            Flags::PROPERLY_SEGMENTED,
+            "is_properly_segmented".to_string(),
+        ),
         SAMScalarUDF::new(Flags::UNMAPPED, "is_unmapped".to_string()),
         SAMScalarUDF::new(Flags::MATE_UNMAPPED, "is_mate_unmapped".to_string()),
         SAMScalarUDF::new(

diff --git a/exon/exon-sam/Cargo.toml b/exon/exon-sam/Cargo.toml
@@ -20,6 +20,6 @@ noodles = { workspace = true, features = [
   "sam",
   "bgzf",
 ] }
-noodles-bgzf = { version = "0.26.0", features = ["libdeflate"] }
+noodles-bgzf = { version = "0.27.0", features = ["libdeflate"] }
 object_store = { workspace = true }
 tokio = { workspace = true }
diff --git a/exon/exon-vcf/Cargo.toml b/exon/exon-vcf/Cargo.toml
@@ -15,6 +15,6 @@ arrow = { workspace = true }
 exon-common = { path = "../exon-common", version = "0.14.0" }
 futures = { workspace = true }
 noodles = { workspace = true, features = ["core", "async", "vcf", "bgzf"] }
-noodles-bgzf = { version = "0.26.0", features = ["libdeflate"] }
+noodles-bgzf = { version = "0.27.0", features = ["libdeflate"] }
 object_store = { workspace = true }
 tokio = { workspace = true }