commit before major update of fastq reader

angelovangel · Dec 9, 2021 · 8283017 · 8283017
1 parent 3d8d2ac
commit 8283017
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Showing 4 changed files with 125 additions and 3 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,4 @@
 /target
 hyperfine.sh 
 mg1655.fasta 
-x86_64-linux
+x86_64_linux*
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -14,6 +14,7 @@ flate2 = "1.0.18"
 clap = "~2.33.3"
 serde_json = "*"
 regex = "1"
+probminhash = "0.1.5"
 
 [dev-dependencies]
 assert_cmd = "0.10"

diff --git a/src/main.rs b/src/main.rs
@@ -12,7 +12,7 @@ use clap::{App, Arg};
 fn get_fastq_reader(path: &String) -> Box<dyn (::std::io::Read)> {
     if path.ends_with(".gz") {
         let f = fs::File::open(path).unwrap();
-        Box::new(bufread::MultiGzDecoder::new(BufReader::new(f)))
+        Box::new(bufread::MultiGzDecoder::new( BufReader::new(f)) )
     } else {
         let f = fs::File::open(path).unwrap();
         Box::new(BufReader::new(f))
@@ -27,7 +27,7 @@ fn main() {
 
         .arg(Arg::with_name("kmer")
         .required(true)
-        .help("k-mer size, maximal value is 21 (required)")
+        .help("k-mer size, maximal value is 31 (required)")
         .takes_value(true)
         .long("kmer_size")
         .short("k"))