From 7240bddb4c4db4da8f88a81ad39cfcf17b94076a Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Mon, 21 Oct 2024 17:20:30 -0400
Subject: [PATCH] add remaining workflow for converting final product to bw

---
 gtars/src/uniwig/mod.rs     | 22 ++++++++++++----------
 gtars/src/uniwig/writing.rs | 22 +++++-----------------
 gtars/tests/test.rs         |  2 +-
 3 files changed, 18 insertions(+), 28 deletions(-)

diff --git a/gtars/src/uniwig/mod.rs b/gtars/src/uniwig/mod.rs
index 2cb9fa79..2ea9ddd2 100644
--- a/gtars/src/uniwig/mod.rs
+++ b/gtars/src/uniwig/mod.rs
@@ -144,9 +144,10 @@ pub fn uniwig_main(
     let ft = FileType::from_str(filetype.to_lowercase().as_str());
     // Set up output file names
 
+    let og_output_type = output_type; // need this later for conversion
     let mut output_type = output_type;
-    if output_type == "bedgraph" {
-        output_type = "bedGraph"
+    if output_type == "bedgraph" || output_type == "bw" || output_type == "bigwig" {
+        output_type = "bedGraph" // we must create bedgraphs first before creating bigwig files
     }
 
     let mut meta_data_file_names: [String; 3] = [
@@ -535,18 +536,19 @@ pub fn uniwig_main(
                 write_combined_files(*location, output_type, bwfileheader, &final_chromosomes);
             }
         }
-        "bw" => {
-            //Ensure bedGraphs files are made and combined before proceeding with bw writing
-            for location in vec_strings.iter() {
-                bar.inc(1);
-                write_combined_files(*location, "bedGraph", bwfileheader, &final_chromosomes);
-            }
+        _ => {}
+    }
+    bar.finish();
 
-            write_bw_files(bwfileheader, chromsizerefpath, num_threads)
+    match og_output_type {
+        "bw" | "bigWig" => {
+            println!("Writing bigWig files");
+            write_bw_files(bwfileheader, chromsizerefpath, num_threads);
         }
+
         _ => {}
     }
-    bar.finish();
+
     println!("FINISHED");
 
     Ok(())
diff --git a/gtars/src/uniwig/writing.rs b/gtars/src/uniwig/writing.rs
index 47693fb6..b8a33858 100644
--- a/gtars/src/uniwig/writing.rs
+++ b/gtars/src/uniwig/writing.rs
@@ -159,11 +159,6 @@ pub fn write_to_bed_graph_file(
 
 /// Converts uniwig generated bedGraphs to bigWig files
 pub fn write_bw_files(location: &str, chrom_sizes: &str, num_threads: i32) {
-    // // Create HashMap to store chromosome information
-    // // Then
-    // let mut chrom_map = HashMap::new();
-    // chrom_map.insert("chr17".to_string(), 83257441);
-
     //Collect all bedGraph files in the given location/directory
     let mut bed_graph_files = Vec::new();
 
@@ -190,28 +185,21 @@ pub fn write_bw_files(location: &str, chrom_sizes: &str, num_threads: i32) {
     println!("bedgraph files {:?}", bed_graph_files);
 
     for file in bed_graph_files.iter() {
-        // let mut path = PathBuf::from(file);
-        // let infile = File::open(file.clone()).unwrap();
-        // let mut vals_iter = BedFileStream::from_bedgraph_file(infile);
-        // //vals_iter.
-        // let test1= vals_iter.next().unwrap().unwrap().1; //this gives a bbi value
-        // println!("done with: {}", file);
-
-        // Just use the built in arg struct and functionbedgraphtobigwig
-
-        let output_name = location.clone(); // TODO
+        let file_path = PathBuf::from(file);
+        let new_file_path = file_path.with_extension("bw");
+        let new_file_path = new_file_path.to_str().unwrap();
 
         let current_arg_struct = BedGraphToBigWigArgs {
             bedgraph: file.to_string(),
             chromsizes: chrom_sizes.to_string(),
-            output: output_name.to_string(),
+            output: new_file_path.to_string(),
             parallel: "".to_string(),
             single_pass: false,
             write_args: BBIWriteArgs {
                 nthreads: num_threads as usize,
                 nzooms: 0,
                 uncompressed: false,
-                sorted: "".to_string(),
+                sorted: "start".to_string(), //TODO CHECK THIS!!!!!!!!!!
                 block_size: 0,
                 items_per_slot: 0,
                 inmemory: false,
diff --git a/gtars/tests/test.rs b/gtars/tests/test.rs
index 135247ee..b7d841fb 100644
--- a/gtars/tests/test.rs
+++ b/gtars/tests/test.rs
@@ -505,7 +505,7 @@ mod tests {
     }
 
     #[rstest]
-    fn test_uniwig_bed_graphs(_path_to_bed_file: &str) {
+    fn test_uniwig_write_bw(_path_to_bed_file: &str) {
         let path_to_crate = env!("CARGO_MANIFEST_DIR");
 
         // Read from sizes file