Add cell hashmap

src/main.rs

@@ -2,7 +2,10 @@ use std::{
     path::Path,
     error::Error,
     fs::File,
+    io::Write,
     io::BufReader,
+    io::BufRead,
+    collections::HashMap,
 };
 use clap::{
     Arg,
@@ -41,7 +44,8 @@ fn main() -> Result<(), Box<dyn Error>> {
             Arg::new("cells")
                 .short('c')
                 .long("cells")
-                .help("List of cells to include"),
+                .help("List of cells to include")
+                .required(true),
         )
         .get_matches();
 
@@ -55,35 +59,54 @@ fn main() -> Result<(), Box<dyn Error>> {
         .expect("Can't find path to input BED file");
     info!("Received BED file: {:?}", bed_file);
 
-    let cell_file = matches.get_one::<String>("cells").map(|cell_path| {
-        Path::new(cell_path)
-            .canonicalize()
-            .expect("Can't find path to input cell file")
-    });
-    if let Some(ref path) = cell_file {
-        info!("Received cell file: {:?}", path);
-    }
+    let cell_file = Path::new(matches.get_one::<String>("cells").unwrap())
+        .canonicalize()
+        .expect("Can't find path to input cell file");
+    info!("Received cell file: {:?}", cell_file);
 
-    fcount(&frag_file, &bed_file, cell_file.as_deref())?;
+    fcount(&frag_file, &bed_file, &cell_file)?;
 
     Ok(())
 }
 
+// TODO add stdout for mtx row,column,value entries
 fn fcount(
     frag_file: &Path,
     bed_file: &Path,
-    cell_file: Option<&Path>,
+    cell_file: &Path,
 ) -> Result<(), Box<dyn Error>> {
     info!(
         "Processing fragment file: {:?}, BED file: {:?}, Cell file: {:?}",
         frag_file, bed_file, cell_file
     );
 
+    // printing to stdout. TODO: change to file output
+    let mut stdout = std::io::stdout().lock();
+    writeln!(stdout, "%%MatrixMarket matrix coordinate integer general").unwrap();
+
+    // tabix file reader
     let mut tbxreader = tabix::io::indexed_reader::Builder::default().build_from_path(frag_file)?;
 
+    // bed file reader
     let mut bedreader = File::open(bed_file)
         .map(BufReader::new)
         .map(bed::io::Reader::new)?;
+
+    //  create hashmap for cell barcodes
+    let cellreader = File::open(cell_file)
+        .map(BufReader::new)?;
+    let mut cells = HashMap::new();
+    for (index, line) in cellreader.lines().enumerate() {
+        let line = line?;
+        cells.insert(line.clone(), index);
+        // writeln!(stdout, "{}", line).unwrap();
+    }
+
+    // create region index variable for matrix row index
+    let mut bed_idx = 1;
+
+    // TODO
+    // might be better to output to a directory rather than stdout as we need the features and cells txt files as well, and to add the matrix dimension to the header
 
     for result in bedreader.records::<3>() {
 
@@ -93,8 +116,21 @@ fn fcount(
         let query = tbxreader.query(&region)?;
         for entry in query {
             let frag_entry = entry?;
-            println!("{}", frag_entry.as_ref());
+
+            // TODO match cell barcodes in hashmap, create vector
+
+            writeln!(stdout, "{}", frag_entry.as_ref()).unwrap();  // placeholder
         }
+
+        // - match cell barcodes in entry to cell barcodes in list
+        // - convert cell barcode to list index
+        // - count fragments per cell barcode
+        // - append row,column,value to mtx file
+        // - increment region index
+        bed_idx = bed_idx + 1;
+
+        // need to track number of nonzero entries (total lines written) and number of bed entries, add this to mtx header at the end?
+
     }
     Ok(())
 }