2024/10/25-09:33:12 (Linux cray unknown)

src/bam.rs

@@ -32,7 +32,7 @@ use crate::bgzf::BgzfReader;
 use crate::genome::Genome;
 use crate::netfile::NetFile;
 use crate::range::Range;
-use crate::reads;
+use crate::read;
 use crate::utility_io::{read_until_null, skip_n_bytes};
 
 /* -------------------------------------------------------------------------- */
@@ -673,7 +673,7 @@ impl<R: Read> BamReader<R> {
         &'a mut self,
         join_pairs: bool,
         paired_end_strand_specific: bool
-    ) -> impl Stream<Item = io::Result<reads::Read>> + 'a {
+    ) -> impl Stream<Item = io::Result<read::Read>> + 'a {
 
         let genome = self.genome.clone();
 
@@ -717,7 +717,7 @@ impl<R: Read> BamReader<R> {
                                 }
                             }
 
-                            yield Ok(reads::Read {
+                            yield Ok(read::Read {
                                 seqname   : seqname,
                                 range     : Range::new(from as usize, to as usize),
                                 strand    : strand as char,
@@ -736,7 +736,7 @@ impl<R: Read> BamReader<R> {
                             let duplicate = r.block1.flag.duplicate();
                             let paired    = r.block1.flag.read_paired();
 
-                            yield Ok(reads::Read {
+                            yield Ok(read::Read {
                                 seqname   : seqname,
                                 range     : Range::new(from as usize, to as usize),
                                 strand    : strand as char,
@@ -776,7 +776,7 @@ impl<R: Read> BamReader<R> {
         &'a mut self,
         join_pairs: bool,
         paired_end_strand_specific: bool
-    ) -> impl Iterator<Item = io::Result<reads::Read>> + 'a {
+    ) -> impl Iterator<Item = io::Result<read::Read>> + 'a {
 
         let s = Box::pin(self.read_simple_stream(join_pairs, paired_end_strand_specific));
 

src/lib.rs

@@ -45,7 +45,7 @@ pub mod granges_sort;
 pub mod infologger;
 pub mod meta;
 pub mod range;
-pub mod reads;
+pub mod read;
 pub mod error;
 pub mod track;
 pub mod track_bed;

src/track_coverage.rs

@@ -29,7 +29,7 @@ use futures::executor::block_on_stream;
 
 use crate::bam::{BamFile, bam_import_genome};
 use crate::genome::Genome;
-use crate::reads;
+use crate::read;
 use crate::infologger::Logger;
 use crate::error::ArgumentError;
 
@@ -265,7 +265,7 @@ pub struct FraglenEstimate {
 
 /* -------------------------------------------------------------------------- */
 
-type ReadStream<'a> = Pin<Box<dyn Stream<Item = io::Result<reads::Read>> + 'a>>;
+type ReadStream<'a> = Pin<Box<dyn Stream<Item = io::Result<read::Read>> + 'a>>;
 
 /* -------------------------------------------------------------------------- */
 

src/track_generic.rs

@@ -23,7 +23,7 @@ use std::collections::HashMap;
 use std::error::Error;
 
 use crate::range::Range;
-use crate::reads::Read;
+use crate::read::Read;
 use crate::track::{MutableTrack, Track};
 use crate::utility::{div_int_up, div_int_down};
 use crate::utility_cumdist::{CumDist, OrderedFloat};

src/track_statistics.rs

@@ -22,7 +22,7 @@ use std::f64;
 use std::error::Error;
 
 use crate::genome::Genome;
-use crate::reads::Read;
+use crate::read::Read;
 use crate::track::Track;
 use crate::track_simple::SimpleTrack;
 use crate::track_generic::GenericMutableTrack;