Set channel size for nthreads == 1 to 0 and trim end

jackh726 · May 14, 2024 · be13c51 · be13c51
1 parent a383b9f
commit be13c51
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Showing 4 changed files with 5 additions and 3 deletions.
diff --git a/bigtools/src/bed/bedparser.rs b/bigtools/src/bed/bedparser.rs
@@ -19,7 +19,7 @@ use crate::bbi::{BedEntry, Value};
 use crate::utils::streaming_linereader::StreamingLineReader;
 
 pub fn parse_bed<'a>(s: &'a str) -> Option<Result<(&'a str, BedEntry), BedValueError>> {
-    let mut split = s.splitn(4, '\t');
+    let mut split = s.trim_end().splitn(4, '\t');
     let chrom = match split.next() {
         Some(chrom) => chrom,
         None => return None,
@@ -47,7 +47,7 @@ pub fn parse_bed<'a>(s: &'a str) -> Option<Result<(&'a str, BedEntry), BedValueE
 }
 
 pub fn parse_bedgraph<'a>(s: &'a str) -> Option<Result<(&'a str, Value), BedValueError>> {
-    let mut split = s.splitn(5, '\t');
+    let mut split = s.trim_end().splitn(5, '\t');
     let chrom = match split.next() {
         Some(chrom) => chrom,
         None => return None,

diff --git a/bigtools/src/bed/indexer.rs b/bigtools/src/bed/indexer.rs
@@ -28,7 +28,7 @@ pub fn index_chroms(file: File) -> io::Result<Option<Vec<(u64, String)>>> {
         if s.is_empty() {
             return Ok(None);
         }
-        let mut split = s.splitn(4, '\t');
+        let mut split = s.trim_end().splitn(4, '\t');
         let chrom = split
             .next()
             .ok_or_else(|| io::Error::new(io::ErrorKind::InvalidData, "Empty file".to_string()))?;

diff --git a/bigtools/src/utils/cli/bedgraphtobigwig.rs b/bigtools/src/utils/cli/bedgraphtobigwig.rs
@@ -87,6 +87,7 @@ pub fn bedgraphtobigwig(args: BedGraphToBigWigArgs) -> Result<(), Box<dyn Error>
         .collect();
 
     let runtime = if nthreads == 1 {
+        outb.options.channel_size = 0;
         runtime::Builder::new_current_thread().build().unwrap()
     } else {
         runtime::Builder::new_multi_thread()

diff --git a/bigtools/src/utils/cli/bedtobigbed.rs b/bigtools/src/utils/cli/bedtobigbed.rs
@@ -96,6 +96,7 @@ pub fn bedtobigbed(args: BedToBigBedArgs) -> Result<(), Box<dyn Error>> {
         .collect();
 
     let runtime = if nthreads == 1 {
+        outb.options.channel_size = 0;
         runtime::Builder::new_current_thread().build().unwrap()
     } else {
         runtime::Builder::new_multi_thread()