feat: add record_context function to prelude

COMBINE-lab · Feb 26, 2024 · aa85018 · aa85018
1 parent 2b2e098
commit aa85018
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Showing 3 changed files with 15 additions and 13 deletions.
diff --git a/examples/read_chunk_bulk.rs b/examples/read_chunk_bulk.rs
@@ -1,8 +1,7 @@
 use anyhow;
 use libradicl;
 use libradicl::chunk::Chunk;
-use libradicl::rad_types;
-use libradicl::record::{PiscemBulkReadRecord, PiscemBulkRecordContext, RecordContext};
+use libradicl::record::{PiscemBulkReadRecord, PiscemBulkRecordContext};
 use std::io::BufReader;
 
 fn main() -> anyhow::Result<()> {
@@ -18,11 +17,7 @@ fn main() -> anyhow::Result<()> {
 
     // Any extra context we may need to parse the records. In this case, it's the
     // size of the barcode and the umi.
-    let tag_context = PiscemBulkRecordContext::get_context_from_tag_section(
-        &p.file_tags,
-        &p.read_tags,
-        &p.aln_tags,
-    )?;
+    let tag_context = p.get_record_context::<PiscemBulkRecordContext>()?;
     let first_chunk = Chunk::<PiscemBulkReadRecord>::from_bytes(&mut ifile, &tag_context);
     println!(
         "Chunk :: nbytes: {}, nrecs: {}",

diff --git a/examples/read_chunk_single_cell.rs b/examples/read_chunk_single_cell.rs
@@ -1,7 +1,7 @@
 use anyhow;
 use libradicl::chunk::Chunk;
 use libradicl::header;
-use libradicl::record::{AlevinFryReadRecord, AlevinFryRecordContext, RecordContext};
+use libradicl::record::{AlevinFryReadRecord, AlevinFryRecordContext};
 use std::io::BufReader;
 
 fn main() -> anyhow::Result<()> {
@@ -17,11 +17,7 @@ fn main() -> anyhow::Result<()> {
     println!("tag map {:?}\n", tag_map);
     // Any extra context we may need to parse the records. In this case, it's the
     // size of the barcode and the umi.
-    let tag_context = AlevinFryRecordContext::get_context_from_tag_section(
-        &p.file_tags,
-        &p.read_tags,
-        &p.aln_tags,
-    )?;
+    let tag_context = p.get_record_context::<AlevinFryRecordContext>()?;
     let first_chunk = Chunk::<AlevinFryReadRecord>::from_bytes(&mut ifile, &tag_context);
     println!(
         "Chunk :: nbytes: {}, nrecs: {}",

diff --git a/src/header.rs b/src/header.rs
@@ -1,5 +1,6 @@
 use crate::{self as libradicl, constants};
 use libradicl::rad_types::{TagSection, TagSectionLabel};
+use libradicl::record::RecordContext;
 use noodles_sam as sam;
 use scroll::Pread;
 use std::io::Read;
@@ -162,4 +163,14 @@ impl RadPrelude {
         //writeln!(&mut s, "file-level tag values [{:?}]", self.file_tag_vals)?;
         Ok(s)
     }
+
+    /// Obtain a [RecordContext] for a record of type `R` from this prelude, by
+    /// using the associated [TagSection]s.  **Note**: Since this function
+    /// constructs the resulting `R` itself, and doesn't take any `R` parameter,
+    /// then it must always be invoked with the proper
+    /// [turbofish](https://doc.rust-lang.org/1.30.0/book/2018-edition/appendix-02-operators.html?highlight=turbofish#non-operator-symbols)
+    /// notation.
+    pub fn get_record_context<R: RecordContext>(&self) -> anyhow::Result<R> {
+        R::get_context_from_tag_section(&self.file_tags, &self.read_tags, &self.aln_tags)
+    }
 }