Update to noodles 0.52.0

zaeleus · Sep 21, 2023 · d6da417 · d6da417
1 parent 2418e9a
commit d6da417
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Showing 6 changed files with 18 additions and 18 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -19,7 +19,7 @@ flate2 = "1.0.14"
 git-testament = "0.2.0"
 interval-tree = { git = "https://github.com/zaeleus/interval-tree.git", rev = "e303d7254d53de5c418d6079d4b66c30c10958d4" }
 mimalloc = { version = "0.1.26", default-features = false }
-noodles = { version = "0.50.0", features = ["bam", "bgzf", "core", "gff", "sam"] }
+noodles = { version = "0.52.0", features = ["bam", "bgzf", "core", "gff", "sam"] }
 noodles-bgzf = { version = "0.24.0", features = ["libdeflate"] }
 thiserror = "1.0.40"
 tracing = "0.1.25"

diff --git a/src/count.rs b/src/count.rs
@@ -129,7 +129,7 @@ pub fn count_single_end_record(
     let start = record.alignment_start()?.expect("missing alignment start");
     let intervals = MatchIntervals::new(&cigar, start);
 
-    let flags = record.flags()?;
+    let flags = record.flags();
     let is_reverse = match strand_specification {
         StrandSpecification::Reverse => !flags.is_reverse_complemented(),
         _ => flags.is_reverse_complemented(),
@@ -254,7 +254,7 @@ pub fn count_paired_end_record_pair(
     let start = r1.alignment_start()?.expect("missing alignment start");
     let intervals = MatchIntervals::new(&cigar, start);
 
-    let f1 = r1.flags()?;
+    let f1 = r1.flags();
     let is_reverse = match strand_specification {
         StrandSpecification::Reverse => !f1.is_reverse_complemented(),
         _ => f1.is_reverse_complemented(),
@@ -271,7 +271,7 @@ pub fn count_paired_end_record_pair(
     let start = r2.alignment_start()?.expect("missing alignment start");
     let intervals = MatchIntervals::new(&cigar, start);
 
-    let f2 = r2.flags()?;
+    let f2 = r2.flags();
     let is_reverse = match strand_specification {
         StrandSpecification::Reverse => f2.is_reverse_complemented(),
         _ => !f2.is_reverse_complemented(),
@@ -308,7 +308,7 @@ pub fn count_paired_end_singleton_record(
     let start = record.alignment_start()?.expect("missing alignment start");
     let intervals = MatchIntervals::new(&cigar, start);
 
-    let flags = record.flags()?;
+    let flags = record.flags();
     let is_reverse = match SegmentPosition::try_from(flags) {
         Ok(SegmentPosition::First) => match strand_specification {
             StrandSpecification::Reverse => !flags.is_reverse_complemented(),

diff --git a/src/count/filter.rs b/src/count/filter.rs
@@ -49,7 +49,7 @@ impl Filter {
     }
 
     pub fn filter(&self, record: &bam::lazy::Record) -> io::Result<Option<Event>> {
-        let flags = record.flags()?;
+        let flags = record.flags();
 
         if flags.is_unmapped() {
             return Ok(Some(Event::Unmapped));
@@ -79,8 +79,8 @@ impl Filter {
         r1: &bam::lazy::Record,
         r2: &bam::lazy::Record,
     ) -> io::Result<Option<Event>> {
-        let f1 = r1.flags()?;
-        let f2 = r2.flags()?;
+        let f1 = r1.flags();
+        let f2 = r2.flags();
 
         if f1.is_unmapped() && f2.is_unmapped() {
             return Ok(Some(Event::Unmapped));

diff --git a/src/detect.rs b/src/detect.rs
@@ -143,7 +143,7 @@ where
     for result in reader.lazy_records().take(MAX_RECORDS) {
         let record = result?;
 
-        let flags = record.flags()?;
+        let flags = record.flags();
 
         if flags.is_unmapped() || flags.is_secondary() || flags.is_supplementary() {
             continue;

diff --git a/src/record_pairs.rs b/src/record_pairs.rs
@@ -80,14 +80,14 @@ where
 }
 
 fn is_not_primary(record: &bam::lazy::Record) -> io::Result<bool> {
-    let flags = record.flags()?;
+    let flags = record.flags();
     Ok(flags.is_secondary() || flags.is_supplementary())
 }
 
 fn key(record: &bam::lazy::Record) -> io::Result<RecordKey> {
     Ok((
         record.read_name().map(|buf| buf.as_ref().to_vec()),
-        SegmentPosition::try_from(record.flags()?)
+        SegmentPosition::try_from(record.flags())
             .map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))?,
         record.reference_sequence_id()?,
         record.alignment_start()?,
@@ -100,7 +100,7 @@ fn key(record: &bam::lazy::Record) -> io::Result<RecordKey> {
 fn mate_key(record: &bam::lazy::Record) -> io::Result<RecordKey> {
     Ok((
         record.read_name().map(|buf| buf.as_ref().to_vec()),
-        SegmentPosition::try_from(record.flags()?)
+        SegmentPosition::try_from(record.flags())
             .map(|p| p.mate())
             .map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))?,
         record.mate_reference_sequence_id()?,