cram/record: Skip unnecessary sequence resolution

The reference sequence is not needed if the record is unmapped or has no sequence.
zaeleus · Feb 18, 2025 · d712d0b · d712d0b
1 parent 087a68b
commit d712d0b
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Showing 2 changed files with 12 additions and 10 deletions.
diff --git a/noodles-cram/src/io/reader/container/slice.rs b/noodles-cram/src/io/reader/container/slice.rs
@@ -136,13 +136,15 @@ impl<'c> Slice<'c> {
 
             record.header = Some(header);
 
-            record.reference_sequence = if reference_sequence_context.is_many() {
-                get_record_reference_sequence(&reference_sequence_repository, header, record)?
-            } else {
-                slice_reference_sequence.clone()
-            };
-
-            record.substitution_matrix = substitution_matrix.clone();
+            if !record.bam_flags.is_unmapped() && !record.cram_flags.sequence_is_missing() {
+                record.reference_sequence = if reference_sequence_context.is_many() {
+                    get_record_reference_sequence(&reference_sequence_repository, header, record)?
+                } else {
+                    slice_reference_sequence.clone()
+                };
+
+                record.substitution_matrix = substitution_matrix.clone();
+            }
         }
 
         resolve_mates(&mut records)?;

diff --git a/noodles-cram/src/record.rs b/noodles-cram/src/record.rs
@@ -143,7 +143,9 @@ impl sam::alignment::Record for Record<'_> {
     }
 
     fn sequence(&self) -> Box<dyn sam::alignment::record::Sequence + '_> {
-        if self.sequence.is_empty() {
+        if self.bam_flags.is_unmapped() || self.cram_flags.sequence_is_missing() {
+            Box::new(Bases(self.sequence))
+        } else {
             let (reference_sequence, alignment_start) = match self.reference_sequence.as_ref() {
                 Some(ReferenceSequence::Embedded {
                     reference_start,
@@ -168,8 +170,6 @@ impl sam::alignment::Record for Record<'_> {
                 alignment_start,
                 self.read_length,
             ))
-        } else {
-            Box::new(Bases(self.sequence))
         }
     }