chore(bam): remove narrative comments

Author: pinin4fjords

src/io/sam.rs

@@ -843,9 +843,6 @@ where
         builder = builder.add_read_group(id, map);
     }
 
-    // @PG line. Per SAM spec §1.3, populate PN/VN/CL alongside ID so downstream
-    // provenance tools (MultiQC program-version table, etc.) see a fully
-    // populated record matching STAR's @PG format.
     let mut pg = Map::<Program>::default();
     pg.other_fields_mut()
         .insert(program_tag::NAME, BString::from("rustar-aligner"));
@@ -1390,8 +1387,6 @@ mod tests {
 
     #[test]
     fn test_build_sam_header_pg_line_populated() {
-        // The @PG line must carry PN, VN and CL alongside ID per SAM spec §1.3,
-        // so downstream provenance tools (MultiQC etc.) get a non-blank entry.
         let genome = make_test_genome();
         let mut params = Parameters::parse_from(vec!["rustar-aligner", "--readFilesIn", "test.fq"]);
         params.command_line =
@@ -1428,8 +1423,6 @@ mod tests {
 
     #[test]
     fn test_build_sam_header_pg_line_default_cl_when_unset() {
-        // When command_line is None (e.g. tests, library use), fall back to
-        // the program name so CL is still non-empty.
         let genome = make_test_genome();
         let params = Parameters::parse_from(vec!["rustar-aligner", "--readFilesIn", "test.fq"]);
         assert!(params.command_line.is_none());

src/params.rs

@@ -702,10 +702,7 @@ pub struct Parameters {
     #[arg(long = "chimOutType", num_args = 1..=2, default_values_t = vec!["Junctions".to_string()])]
     pub chim_out_type: Vec<String>,
 
-    /// Full command line as invoked (captured in `main` before clap parsing).
-    /// Not a CLI argument; populated programmatically and embedded in the
-    /// BAM `@PG` `CL:` field for provenance. STAR captures the same string
-    /// in `P.commandLineFull`.
+    /// Full command line as invoked, embedded in the BAM `@PG` `CL:` field.
     #[arg(skip)]
     pub command_line: Option<String>,
 }