scan remove chrM

src/callers/mod.rs

@@ -287,7 +287,7 @@ pub fn run_chunkeds(id: &str, config: &Config) -> anyhow::Result<()> {
     DeepSomatic::initialize(id, config)?.run()?;
 
     // Mutect2 - somatic SNV/indels caller
-    Mutect2::initialize(id, config)?.run()?;
+    // Mutect2::initialize(id, config)?.run()?;
 
     // DeepVariant - germline variants for normal sample
     DeepVariant::initialize(id, &config.normal_name, config)?.run()?;

src/collection/bam_stats.rs

@@ -1359,7 +1359,7 @@ mod tests {
 
         let config = Config::default();
 
-        let stats = WGSBamStats::open("CHAHA", "diag", &config)?;
+        let stats = WGSBamStats::open("NORCL", "diag", &config)?;
         println!("{stats}");
         // let stats = WGSBamStats::open("36434", "norm", &config)?;
         // println!("{stats}");

src/io/bam.rs

@@ -817,16 +817,16 @@ pub fn read_sm_tag_or_inject(
         // At least one @RG line missing SM — inject into those
         info!("Some @RG lines in {bam_path} lack SM tag, injecting SM:{fallback_sample}");
 
-        let original_mtime = filetime::FileTime::from_last_modification_time(
-            &std::fs::metadata(bam_path)?,
-        );
-
-        let mut reheader = SamtoolsReheader::from_config(config, bam_path, fallback_sample);
-        reheader.run()?;
-        let mut index = SamtoolsIndex::from_config(config, bam_path);
-        index.run()?;
-
-        filetime::set_file_mtime(bam_path, original_mtime)?;
+        // let original_mtime = filetime::FileTime::from_last_modification_time(
+        //     &std::fs::metadata(bam_path)?,
+        // );
+        //
+        // let mut reheader = SamtoolsReheader::from_config(config, bam_path, fallback_sample);
+        // reheader.run()?;
+        // let mut index = SamtoolsIndex::from_config(config, bam_path);
+        // index.run()?;
+        //
+        // filetime::set_file_mtime(bam_path, original_mtime)?;
 
         return Ok(first_sm.unwrap_or_else(|| fallback_sample.to_string()));
     }