Merge pull request #5 from sapporo-wes/enhancement/1

add support for STDIN and compressed format (gzip, bz2)

src/args.rs

@@ -49,12 +49,11 @@ pub struct Args {
     #[clap(short, long, conflicts_with_all = ["num_records"])]
     pub tidy: bool,
 
-    // TODO
     /// Do not try to decompress the input file when detecting the file format.
-    #[clap(long, hide = true)]
+    #[clap(long)]
     pub no_decompress: bool,
 
-    /// Number of records to read from the input file. Conflicts with `--tidy` option.
+    /// Number of records to read from the input file. Recommened to set it to a multiple of 4 to prevent false negatives. Conflicts with `--tidy` option.
     #[clap(short, long, default_value = "100000", value_parser = validate_num_records_greater_than_zero)]
     pub num_records: usize,
 

src/buffered_read_seek.rs

@@ -19,21 +19,20 @@ impl<R: Read> OnetimeRewindableReader<R> {
 impl<R: Read> Read for OnetimeRewindableReader<R> {
     fn read(&mut self, buf: &mut [u8]) -> io::Result<usize> {
         if let Some(ref mut buffer) = self.buffer {
-            // 既にバッファがある場合はそこから読み取る
+            // read from the buffer if it exists
             let count = buffer.read(buf)?;
             if count == 0 {
-                // バッファが空になった場合は、元の入力から読み取る
-                let innercount = self.inner.read(buf);
-                innercount
+                // if the buffer is empty, read from the original input
+                self.inner.read(buf)
             } else {
                 Ok(count)
             }
         } else {
-            // 初回の読み取りでバッファを準備
+            // Prepare the buffer for the first read
             let mut temp_buffer = vec![0; buf.len()];
             let count = self.inner.read(&mut temp_buffer)?;
             if count > 0 {
-                // 読み取ったデータをバッファとして保存
+                // save the read data as a buffer
                 self.buffer = Some(Cursor::new(temp_buffer));
                 self.read(buf)
             } else {

src/edam.rs

@@ -63,6 +63,7 @@ impl EdamMap {
     }
 }
 
+// A internal struct to deserialize EDAM table.
 #[derive(Debug, Clone, Deserialize)]
 struct Edam {
     #[serde(rename = "Class ID")]

src/ext_tools.rs

@@ -17,7 +17,7 @@ pub fn invoke(
     cwl_file_path: &Path,
     target_file_path: &Path,
     cwl_input_file_path: &NamedTempFile,
-    options: &InvokeOptions,
+    _options: &InvokeOptions,
 ) -> Result<ModuleResult> {
     info!("Invoking ext_tools {}", cwl_file_path.display());