From febeb9706e02de04bc098e4e006704c9f25df8d3 Mon Sep 17 00:00:00 2001
From: chris <chris.ieng@mcri.edu.au>
Date: Tue, 1 Jul 2025 14:55:46 +1000
Subject: [PATCH] remove unnecessary clone of orig as can be moved. refactor
 merges to use MergeType enum and separate method

---
 src/merge.rs | 109 ++++++++++++++++++++++++++++++++++-----------------
 1 file changed, 74 insertions(+), 35 deletions(-)

diff --git a/src/merge.rs b/src/merge.rs
index 4589176..30fb71b 100644
--- a/src/merge.rs
+++ b/src/merge.rs
@@ -14,7 +14,7 @@ use datafusion::{
     common::JoinType,
     functions_aggregate::expr_fn::first_value,
     prelude::{
-        DataFrame, cast, col, concat, concat_ws, encode, left, length, lit, nullif, sha256, to_hex,
+        cast, col, concat, concat_ws, encode, left, length, lit, nullif, sha256, to_hex, DataFrame, SessionContext
     },
 };
 use noodles::{
@@ -47,6 +47,15 @@ mod flip;
 mod report;
 mod union;
 
+enum MergeType {
+    Exact,
+    Locus,
+    ExactBreakend,
+    Approx,
+    Near,
+    Flip,
+}
+
 pub async fn merge_vcfs(
     out: &str,
     vcf: &Vec<String>,
@@ -85,46 +94,30 @@ pub async fn merge_vcfs(
             acc = Some(df)
         }
     }
-    let orig = acc.unwrap();
-    let orig = orig
+    let results = acc.unwrap();
+    let mut results = results
         .with_column("row_key", cast(col("row_id"), DataType::UInt32))?
         .with_column("vix_count", lit(1))?
         .with_column("vix_set", col("vix"))?
         .with_column("flip", lit(false))?
         .with_column("criteria", nullif(lit(""), lit("")))?;
 
-    let mut results = orig.clone();
-
-    if true {
-        log::info!("looking for exact matches on indel type variants");
-        let join = full_exact_indel_join(results.clone(), n)?;
-        results = merge_with(results, join, &ctx, "exact").await?;
-    }
-    if true {
-        log::info!("looking for almost exact matches on insertions");
-        let join = full_exact_locus_ins_join(results.clone(), n, &options)?;
-        results = merge_with(results, join, &ctx, "locus").await?;
-    }
-    if true {
-        log::info!("looking for exact matches on breakends");
-        let join = full_exact_bnd(results.clone(), n)?;
-        results = merge_with(results, join, &ctx, "exact").await?;
-    }
-    if true {
-        log::info!("looking for approximate matches on breakends");
-        let join = approx_bnd_join(results.clone(), n, &options)?;
-        results = merge_with(results, join, &ctx, "approx").await?;
-    }
-    if true {
-        log::info!("looking for nearby matches on indel type variants");
-        let join = approx_near_join(results.clone(), n, &options, &ctx).await?;
-        results = merge_with(results, join, &ctx, "near").await?;
-    }
-    if options.allow_breakend_flipping {
-        log::info!("looking for breakends we can flip");
-        let join = approx_flipped_bnd_join(results.clone(), n, &options)?;
-        results = merge_with(results, join, &ctx, "flip").await?;
-    }
+    let enabled_merges = vec![
+        MergeType::Exact,
+        MergeType::Locus,
+        MergeType::ExactBreakend,
+        MergeType::Approx,
+        MergeType::Near,
+        MergeType::Flip,
+    ];
+
+    results = apply_enabled_merges(
+        results,
+        &enabled_merges,
+        n,
+        &options,
+        &ctx,
+    ).await?;
 
     let mut reference = None;
     if let Some(reference_filename) = &options.reference {
@@ -382,6 +375,52 @@ pub async fn merge_vcfs(
     Ok(())
 }
 
+async fn apply_enabled_merges(
+    mut results: DataFrame,
+    enabled_merges: &[MergeType],
+    n: usize,
+    options: &MergeOptions,
+    ctx: &SessionContext,
+) -> std::io::Result<DataFrame> {
+    for m in enabled_merges {
+        match m {
+            MergeType::Exact => {
+                log::info!("looking for exact matches on indel type variants");
+                let join = full_exact_indel_join(results.clone(), n)?;
+                results = merge_with(results, join, &ctx, "exact").await?;
+            }
+            MergeType::Locus => {
+                log::info!("looking for almost exact matches on insertions");
+                let join = full_exact_locus_ins_join(results.clone(), n, &options)?;
+                results = merge_with(results, join, &ctx, "locus").await?;
+            }
+            MergeType::ExactBreakend => {
+                log::info!("looking for exact matches on breakends");
+                let join = full_exact_bnd(results.clone(), n)?;
+                results = merge_with(results, join, &ctx, "exact").await?;
+            }
+            MergeType::Approx =>{
+                log::info!("looking for approximate matches on breakends");
+                let join = approx_bnd_join(results.clone(), n, &options)?;
+                results = merge_with(results, join, &ctx, "approx").await?;
+            }
+            MergeType::Near => {
+                log::info!("looking for nearby matches on indel type variants");
+                let join = approx_near_join(results.clone(), n, &options, &ctx).await?;
+                results = merge_with(results, join, &ctx, "near").await?;
+            }
+            MergeType::Flip => {
+                if options.allow_breakend_flipping {
+                    log::info!("looking for breakends we can flip");
+                    let join = approx_flipped_bnd_join(results.clone(), n, &options)?;
+                    results = merge_with(results, join, &ctx, "flip").await?;
+                }
+            }
+        }
+    }
+    Ok(results)
+}
+
 fn load_chroms(path: &str) -> std::io::Result<ChromSet> {
     let reader = autocompress::autodetect_open(path)?;
     let mut reader: vcf::io::Reader<Box<dyn BufRead>> =