cleanup IO.pm and add tests

bystrogenomics · Feb 21, 2024 · 961300c · 961300c
1 parent 54fdf9b
commit 961300c
Show file tree

Hide file tree

Showing 4 changed files with 374 additions and 151 deletions.
diff --git a/perl/lib/Seq.pm b/perl/lib/Seq.pm
@@ -471,8 +471,7 @@ sub _preparePreprocessorProgram {
 
   my $errPath = $self->_workingDir->child( $basename . '.file-log.log' );
 
-  #cat is wasteful, but we expect no one reads large uncompressed files
-  my $echoProg = $self->getReadArgs($inPath) || "cat $inPath";
+  my $echoProg = $self->getReadArgs($inPath);
 
   my $fp = $self->fileProcessors->{$type};