tweak dais file reading to ignore the gen files

Author: mandysulli

src/processes/prepare_mira_reports.rs

@@ -155,10 +155,11 @@ pub fn prepare_mira_reports_process(args: ReportsArgs) -> Result<(), Box<dyn Err
         }));
 
     //Read in DAIS-ribosome data
-    //let dais_ins_data = dais_insertion_data_collection(&args.irma_path)?;
-    //let dais_del_data = dias_deletion_data_collection(&args.irma_path)?;
-    //let dais_seq_data = dias_sequence_data_collection(&args.irma_path)?;
-    //let dais_ref_data = dais_ref_seq_data_collection(&args.workdir_path, virus)?;
+    let dais_ins_data = dais_insertion_data_collection(&args.irma_path)?;
+    let dais_del_data = dias_deletion_data_collection(&args.irma_path)?;
+    let dais_seq_data = dias_sequence_data_collection(&args.irma_path)?;
+    //TODO: sc2 handling
+    let dais_ref_data = dais_ref_seq_data_collection(&args.workdir_path, &args.virus)?;
 
     //TODO: remove these at end
     //println!("{qc_config:?}")
@@ -174,7 +175,7 @@ pub fn prepare_mira_reports_process(args: ReportsArgs) -> Result<(), Box<dyn Err
 
     //Calculate AA variants for aavars.csv and dais_vars.json
     //TODO: circle back for the rsv and sc2 situations
-    //let dais_vars_data = compute_dais_variants(&dais_ref_data, &dais_seq_data)?;
+    let dais_vars_data = compute_dais_variants(&dais_ref_data, &dais_seq_data)?;
     negative_qc_statement(
         "/home/xpa3/mira-oxide/test/qc_statement.json",
         &read_data,

src/utils/data_ingest.rs

@@ -677,7 +677,7 @@ pub fn dais_insertion_data_collection(
     // Construct the glob pattern for matching files
     //If using * situation, you will have to use glob
     let pattern = format!(
-        "{}/aggregate_outputs/dais-ribosome/*.ins",
+        "{}/aggregate_outputs/dais-ribosome/DAIS_ribosome.ins",
         dais_path.as_ref().display()
     );
 
@@ -708,7 +708,7 @@ pub fn dias_deletion_data_collection(
     // Construct the glob pattern for matching files
     //If using * situation, you will have to use glob
     let pattern = format!(
-        "{}/aggregate_outputs/dais-ribosome/*.del",
+        "{}/aggregate_outputs/dais-ribosome/DAIS_ribosome.del",
         dais_path.as_ref().display()
     );
 
@@ -728,7 +728,6 @@ pub fn dias_deletion_data_collection(
             }
         }
     }
-
     Ok(dais_del_data)
 }
 
@@ -739,7 +738,7 @@ pub fn dias_sequence_data_collection(
     // Construct the glob pattern for matching files
     //If using * situation, you will have to use glob
     let pattern = format!(
-        "{}/aggregate_outputs/dais-ribosome/*.seq",
+        "{}/aggregate_outputs/dais-ribosome/DAIS_ribosome.seq",
         dais_path.as_ref().display()
     );