save to scan to file

src/lib.rs

@@ -6,12 +6,14 @@ use log::info;
 use rust_htslib::bam::{Format, Header, Read, Record, Writer};
 use std::{
     collections::{HashMap, HashSet},
-    fs,
+    fs::{self, File},
+    io::{BufWriter, Write},
 };
 
 pub mod bam;
 pub mod bin;
 
+#[allow(clippy::too_many_arguments)]
 pub fn scan_save(
     diag_bam_path: &str,
     contig: &str,
@@ -19,13 +21,17 @@ pub fn scan_save(
     end: u32,
     bin_length: u32,
     min_reads: usize,
-    out_dir: &str,
+    out_scan_file: &str,
+    out_dir_bam: &str,
 ) -> anyhow::Result<()> {
+    let out_scan = File::create(out_scan_file).expect("Failed to create file");
+    let mut writer = BufWriter::new(out_scan);
+
     let outliers_records: Vec<Vec<Record>> =
         scan_outliers(diag_bam_path, contig, start, end, bin_length)
             .iter()
             .filter(|(_, _, _, sa_outlier, _, se_outlier)| *sa_outlier || *se_outlier)
-            .map(|(start, _n, _sa, sa_outlier, _se, se_outlier)| {
+            .map(|(start, n, sa, sa_outlier, se, se_outlier)| {
                 let mut bin = Bin::new(diag_bam_path, contig, *start, bin_length).unwrap();
                 let mut records = Vec::new();
                 if *sa_outlier {
@@ -34,12 +40,16 @@ pub fn scan_save(
                     let (pos, _) = bin.max_start_or_end();
                     records.extend(bin.se_primary(pos));
                 };
-                // info!(
-                //     "{}:{start}-{}\t{n}\t{sa}\t{se}\t{}",
-                //     contig,
-                //     start + bin_length - 1,
-                //     records.len()
-                // );
+                writeln!(
+                    writer,
+                    "{}:{start}-{}\t{n}\t{sa}\t{}\t{se}\t{}\t{}",
+                    contig,
+                    start + bin_length - 1,
+                    sa_outlier,
+                    se_outlier,
+                    records.len(),
+                )
+                .unwrap();
                 records
             })
             .collect();
@@ -105,7 +115,7 @@ pub fn scan_save(
         .map(|r| r.to_vec())
         .collect();
 
-    fs::create_dir_all(out_dir).unwrap();
+    fs::create_dir_all(out_dir_bam).unwrap();
 
     info!(
         "{} reads to assemble in {} groups",
@@ -115,7 +125,7 @@ pub fn scan_save(
 
     let header = Header::from_template(&header);
     for records in grouped_records {
-        let output_bam_path = format!("{out_dir}/{}.bam", uuid::Uuid::new_v4());
+        let output_bam_path = format!("{out_dir_bam}/{}.bam", uuid::Uuid::new_v4());
         let mut output_bam = Writer::from_path(output_bam_path, &header, Format::Bam).unwrap();
         for record in records {
             output_bam.write(&record)?;
@@ -146,6 +156,7 @@ mod tests {
         let result_dir = "/data/longreads_basic_pipe";
         let diag_bam_path = format!("{result_dir}/{id}/diag/{id}_diag_hs1.bam");
         let out_dir = format!("/data/tmp/scan_{}", uuid::Uuid::new_v4());
+        let out_scan_file = "/data/tmp/scan.tsv";
 
         scan_save(
             &diag_bam_path,
@@ -154,6 +165,7 @@ mod tests {
             end,
             bin_length,
             min_reads,
+            out_scan_file,
             &out_dir,
         )?;
         let n_files_out = fs::read_dir(out_dir).into_iter().count();