2024/10/25-15:04:18 (Linux cray unknown)

pbenner · Oct 25, 2024 · 4eeb297 · 4eeb297
1 parent ea5edbe
commit 4eeb297
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Showing 4 changed files with 25 additions and 29 deletions.
diff --git a/src/track.rs b/src/track.rs
@@ -129,6 +129,7 @@ pub trait Track {
 
 pub trait MutableTrack : Track {
     fn as_track(&self) -> &dyn Track;
+    fn filter_genome(&mut self, f: &dyn Fn(&str, usize) -> bool);
     fn get_sequence_mut(&mut self, seqname: &str) -> Result<TrackMutableSequence, Box<dyn Error>>;
 }
 

diff --git a/src/track_generic_coverage.rs b/src/track_generic_coverage.rs
@@ -23,7 +23,6 @@ use std::error::Error;
 use futures::executor::block_on_stream;
 
 use crate::coverage::CoverageConfig;
-use crate::genome::Genome;
 use crate::read_stream::ReadStream;
 use crate::track_generic::GenericMutableTrack;
 use crate::bam::BamFile;
@@ -34,13 +33,12 @@ impl<'a> GenericMutableTrack<'a> {
 
     pub fn coverage_from_bam(
         mut config         : CoverageConfig,
-        track1             : GenericMutableTrack,
+        mut track1         : GenericMutableTrack,
         track2_arg         : Option<GenericMutableTrack>,
         filenames_treatment: &Vec<&str>,
         filenames_control  : &Vec<&str>,
         fraglen_treatment  : &Vec<usize>,
         fraglen_control    : &Vec<usize>,
-        genome             : Genome,
     ) -> Result<(), Box<dyn Error>> {
         // Treatment data
         let mut n_treatment = 0;
@@ -97,7 +95,7 @@ impl<'a> GenericMutableTrack<'a> {
             config.pseudocounts[0] *= c;
         }
 
-        if let Some(track2) = track2_arg {
+        if let Some(mut track2) = track2_arg {
             // Control data
 
             for (i, filename) in filenames_control.iter().enumerate() {
@@ -174,7 +172,7 @@ impl<'a> GenericMutableTrack<'a> {
         if config.remove_filtered_chroms {
             if !config.filter_chroms.is_empty() {
                 log!(config.logger, "Removing chromosomes `{}`", config.filter_chroms.join(", "));
-                track1.filter_genome(|name, _length| {
+                track1.track.filter_genome(&|name : &str, _length : usize| {
                     !config.filter_chroms.contains(&name.to_string())
                 });
             }

diff --git a/src/track_simple.rs b/src/track_simple.rs
@@ -98,26 +98,6 @@ impl SimpleTrack {
         position / self.bin_size
     }
 
-    pub fn filter_genome<F>(&mut self, f: F)
-    where
-        F: Fn(&str, usize) -> bool,
-    {
-        let retain_seqnames: Vec<String> = self
-            .data
-            .keys()
-            .filter(|seqname| {
-                let idx = self.genome.seqnames.iter().position(|x| x == *seqname).unwrap();
-                f(seqname, self.genome.lengths[idx])
-            })
-            .cloned()
-            .collect();
-
-        // Retain the seqnames in self.data
-        self.data.retain(|seqname, _| retain_seqnames.contains(seqname));
-
-        // Perform the filtering on genome
-        self.genome.filter(f);
-    }
 }
 
 /* -------------------------------------------------------------------------- */
@@ -195,6 +175,25 @@ impl MutableTrack for SimpleTrack {
         self
     }
 
+    fn filter_genome(&mut self, f: &dyn Fn(&str, usize) -> bool)
+    {
+        let retain_seqnames: Vec<String> = self
+            .data
+            .keys()
+            .filter(|seqname| {
+                let idx = self.genome.seqnames.iter().position(|x| x == *seqname).unwrap();
+                f(seqname, self.genome.lengths[idx])
+            })
+            .cloned()
+            .collect();
+
+        // Retain the seqnames in self.data
+        self.data.retain(|seqname, _| retain_seqnames.contains(seqname));
+
+        // Perform the filtering on genome
+        self.genome.filter(f);
+    }
+
     fn get_sequence_mut(&mut self, query: &str) -> Result<TrackMutableSequence, Box<dyn Error>> {
         match self.data.get_mut(query) {
             Some(seq) => Ok(TrackMutableSequence::new(seq.clone(), self.bin_size)),

diff --git a/src/track_simple_coverage.rs b/src/track_simple_coverage.rs
@@ -50,8 +50,7 @@ impl SimpleTrack {
                 filenames_treatment,
                 filenames_control,
                 fraglen_treatment,
-                fraglen_control,
-                genome)?;
+                fraglen_control)?;
 
         } else {
 
@@ -62,8 +61,7 @@ impl SimpleTrack {
                 filenames_treatment,
                 filenames_control,
                 fraglen_treatment,
-                fraglen_control,
-                genome)?;
+                fraglen_control)?;
 
         };