chore(derive): disable index checking when not needed

stjude-rust-labs · Dec 16, 2023 · 55ee258 · 55ee258
1 parent 81511e2
commit 55ee258
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/src/derive/command/endedness.rs b/src/derive/command/endedness.rs
@@ -74,7 +74,7 @@ pub fn derive(args: DeriveEndednessArgs) -> anyhow::Result<()> {
 
     let ParsedBAMFile {
         mut reader, header, ..
-    } = crate::utils::formats::bam::open_and_parse(args.src, IndexCheck::Full)?;
+    } = crate::utils::formats::bam::open_and_parse(args.src, IndexCheck::None)?;
 
     // (1) Collect read lengths from reads within the
     // file. Support for sampling only a portion of the reads is provided.

diff --git a/src/derive/command/instrument.rs b/src/derive/command/instrument.rs
@@ -56,7 +56,7 @@ async fn app(src: PathBuf, first_n_reads: Option<usize>) -> anyhow::Result<()> {
 
     let ParsedBAMFile {
         mut reader, header, ..
-    } = crate::utils::formats::bam::open_and_parse(src, IndexCheck::Full)?;
+    } = crate::utils::formats::bam::open_and_parse(src, IndexCheck::None)?;
 
     // (1) Collect instrument names and flowcell names from reads within the
     // file. Support for sampling only a portion of the reads is provided.

diff --git a/src/derive/command/readlen.rs b/src/derive/command/readlen.rs
@@ -50,7 +50,7 @@ pub fn derive(args: DeriveReadlenArgs) -> anyhow::Result<()> {
 
     let ParsedBAMFile {
         mut reader, header, ..
-    } = crate::utils::formats::bam::open_and_parse(args.src, IndexCheck::Full)?;
+    } = crate::utils::formats::bam::open_and_parse(args.src, IndexCheck::None)?;
 
     // (1) Collect read lengths from reads within the
     // file. Support for sampling only a portion of the reads is provided.