Put back gz file name detection.

Using probeContentType is just too fragile - it breaks everywhere except linux. Bump version to 0.12.1
s-andrews · Mar 1, 2023 · 2b74369 · 2b74369
1 parent e5c3505
commit 2b74369
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/uk/ac/babraham/FastQC/FastQCApplication.java b/uk/ac/babraham/FastQC/FastQCApplication.java
@@ -54,7 +54,7 @@
 
 public class FastQCApplication extends JFrame {	
 
-	public static final String VERSION = "0.12.0";
+	public static final String VERSION = "0.12.1";
 
 	private JTabbedPane fileTabs;
 	private WelcomePanel welcomePanel;

diff --git a/uk/ac/babraham/FastQC/Sequence/FastQFile.java b/uk/ac/babraham/FastQC/Sequence/FastQFile.java
@@ -72,14 +72,15 @@ protected FastQFile(FastQCConfig config,File file) throws SequenceFormatExceptio
 			}
 		}
 
+		System.out.println(Files.probeContentType(file.toPath()));
 		if (!file.getName().startsWith("stdin")) {
 			fis = new FileInputStream(file);
 		}
 
 		if (file.getName().startsWith("stdin")) {
 			br = new BufferedReader(new InputStreamReader(System.in));
 		}
-		else if (Files.probeContentType(file.toPath()) != null && (Files.probeContentType(file.toPath()).equals("application/x-gzip") || Files.probeContentType(file.toPath()).equals("application/gzip"))) {
+		else if (file.getName().toLowerCase().endsWith(".gz") || (Files.probeContentType(file.toPath()) != null && (Files.probeContentType(file.toPath()).equals("application/x-gzip") || Files.probeContentType(file.toPath()).equals("application/gzip")))) {
 			br = new BufferedReader(new InputStreamReader(new MultiMemberGZIPInputStream(fis)));
 		} 
 		else if (file.getName().toLowerCase().endsWith(".bz2")) {