updating summary pass fail logic

Author: mandysulli

src/processes/prepare_mira_reports.rs

@@ -10,14 +10,11 @@ use crate::utils::{
     data_processing::{
         DaisVarsData, ProcessedCoverage, Subtype, collect_analysis_metadata, collect_negatives,
         collect_sample_id, compute_cvv_dais_variants, compute_dais_variants,
-        create_final_irma_summary_df, create_prelim_irma_summary_df, create_vtype_data,
-        extract_field, extract_subtype_flu, extract_subtype_sc2, melt_reads_data,
-        process_position_coverage_data, process_wgs_coverage_data, return_seg_data,
-    },
-    writing_outputs::{
-        negative_qc_statement, write_reads_to_parquet, write_ref_data_json,
-        write_structs_to_csv_file, write_structs_to_split_json_file,
+        create_prelim_irma_summary_df, create_vtype_data, extract_field, extract_subtype_flu,
+        extract_subtype_sc2, melt_reads_data, process_position_coverage_data,
+        process_wgs_coverage_data, return_seg_data,
     },
+    writing_outputs::negative_qc_statement,
 };
 use clap::Parser;
 use csv::ReaderBuilder;
@@ -267,15 +264,16 @@ pub fn prepare_mira_reports_process(args: ReportsArgs) -> Result<(), Box<dyn Err
         }
     }
 
-    let irma_summary =
-        create_final_irma_summary_df(&irma_summary, &dais_vars_data, &seq_data, qc_values);
+    for sample in &mut irma_summary {
+        sample.create_final_irma_summary_df(&dais_vars_data, &seq_data, &qc_values);
+    }
     //println!("{qc_values:?}");
     //todo:remove before end
     //println!("{dais_vars_data:?}");
     //println!("{melted_reads_df:?}");
     //println!("{calculated_cov_df:?}");
     //println!("{calculated_position_cov_df:?}");
-    //println!("{irma_summary:?}");
+    println!("{irma_summary:?}");
     //println!("{subtype_data:?}");
 
     /////////////////////////////////////////////////////////////////////////////

src/utils/data_ingest.rs

@@ -232,7 +232,7 @@ pub struct DaisSeqData {
     #[serde(rename = "ID")]
     pub sample_id: Option<String>,
     #[serde(rename = "C_type")]
-    pub ctype: Option<String>,
+    pub ctype: String,
     #[serde(rename = "Ref_ID")]
     pub reference: String,
     #[serde(rename = "Protein")]

src/utils/data_processing.rs

@@ -27,6 +27,7 @@ pub struct ProcessedRecord {
 #[derive(Serialize, Deserialize, Debug)]
 pub struct DaisVarsData {
     pub sample_id: Option<String>,
+    pub ctype: String,
     pub reference_id: String,
     pub protein: String,
     pub aa_variant_count: i32,
@@ -359,6 +360,7 @@ pub fn compute_dais_variants(
 
                 let dais_vars_entry = DaisVarsData {
                     sample_id: sample_entry.sample_id.clone(),
+                    ctype: sample_entry.ctype.clone(),
                     reference_id: sample_entry.reference.clone(),
                     protein: sample_entry.protein.clone(),
                     aa_variant_count: var_aa_count,
@@ -430,6 +432,7 @@ pub fn compute_cvv_dais_variants(
         .into_values()
         .map(|entry| DaisVarsData {
             sample_id: entry.sample_id,
+            ctype: entry.ctype,
             reference_id: entry.reference.clone(),
             protein: entry.protein.clone(),
             aa_variant_count: entry.insertions_shift_frame.parse::<i32>().unwrap_or(0),
@@ -987,14 +990,32 @@ pub fn create_prelim_irma_summary_df(
 }
 
 /// Combine all df to create IRMA summary
-pub fn create_final_irma_summary_df(
-    prelim_sumamary: &[IRMASummary],
-    dais_vars: &[DaisVarsData],
-    seq_df: &[SeqData],
-    qc_values: QCSettings,
-) -> Result<Vec<IRMASummary>, Box<dyn Error>> {
-    let mut irma_summary: Vec<IRMASummary> = Vec::new();
-    println!("QC {qc_values:#?}");
 
-    Ok(irma_summary)
+impl IRMASummary {
+    pub fn create_final_irma_summary_df(
+        &mut self,
+        dais_vars: &[DaisVarsData],
+        seq_df: &[SeqData],
+        qc_values: &QCSettings,
+    ) -> Result<Vec<IRMASummary>, Box<dyn Error>> {
+        let mut irma_summary: Vec<IRMASummary> = Vec::new();
+        println!("QC {qc_values:#?}");
+        println!("QC {dais_vars:#?}");
+
+        let mut premature_stop_codon_df = String::new();
+        if !qc_values.allow_stop_codons {
+            for entry in dais_vars {
+                if self.sample_id == entry.sample_id
+                    && self.reference == Some(entry.ctype.clone())
+                    && entry.aa_variants.contains('*')
+                {
+                    self.pass_fail_reason =
+                        format!("Premature stop codon '{}'", entry.protein).into();
+                }
+            }
+        }
+        //println!("{premature_stop_codon_df}");
+
+        Ok(irma_summary)
+    }
 }