Add ability to read bw files and return maximum value across an interval

gtars/src/uniwig/mod.rs

@@ -38,7 +38,7 @@ use tokio::runtime;
 pub mod cli;
 pub mod counting;
 pub mod reading;
-mod utils;
+pub mod utils;
 pub mod writing;
 
 pub mod consts {

gtars/src/uniwig/utils.rs

@@ -1,6 +1,31 @@
+use bigtools::{BigWigRead, BigWigReadOpenError};
+use bigtools::utils::reopen::ReopenableFile;
 use crate::uniwig::reading::{read_bed_vec, read_narrow_peak_vec};
 use crate::uniwig::{Chromosome, FileType};
 
+
+
+/// Read in bigwig file and return as object.
+pub fn read_bw_file(path_to_bw: &str) -> Result<BigWigRead<ReopenableFile>, BigWigReadOpenError> {
+    let bigwig = BigWigRead::open_file(path_to_bw);
+
+    bigwig
+
+}
+
+/// Get maximum value across an interval over a specific chromosome within a bigwig file
+pub fn get_max_val_chr_bw(mut bigwig: BigWigRead<ReopenableFile>, chr_name: &str, start: u32, end: u32) -> Option<f32> {
+
+    let bw_values = bigwig.values(chr_name,start,end).unwrap();
+
+    let max = bw_values.into_iter()
+        .reduce(f32::max)
+        ;
+
+    max
+}
+
+
 /// Attempt to compress counts before writing to bedGraph
 pub fn compress_counts(
     count_results: &mut (Vec<u32>, Vec<i32>),

gtars/tests/test.rs

@@ -14,6 +14,11 @@ fn path_to_bed_file() -> &'static str {
     "tests/data/peaks.bed"
 }
 
+#[fixture]
+fn path_to_bw_file() -> &'static str {
+    "tests/data/test_all_core.bw"
+}
+
 #[fixture]
 fn path_to_sorted_small_bed_file() -> &'static str {
     "tests/data/test_sorted_small.bed"
@@ -87,6 +92,7 @@ mod tests {
     };
 
     use gtars::uniwig::writing::write_bw_files;
+    use gtars::uniwig::utils::{get_max_val_chr_bw, read_bw_file};
 
     use anyhow::Context;
     use byteorder::{LittleEndian, ReadBytesExt};
@@ -1115,4 +1121,18 @@ mod tests {
 
         Ok(())
     }
+
+
+    #[rstest]
+    fn test_read_bw_and_get_max(
+        path_to_bw_file: &str,
+    ) {
+        let bw_path = path_to_bw_file;
+
+        let bw_info = read_bw_file(bw_path).unwrap();
+
+        let max =  get_max_val_chr_bw(bw_info, "chr1",0,29).unwrap();
+
+        assert_eq!(max, 4.0);
+    }
 }