bugfixes (minor-no issue tickets)

Author: owlang

src/main/java/scriptmanager/cli/Peak_Analysis/SortByDistCLI.java

@@ -40,7 +40,7 @@ public class SortByDistCLI implements Callable<Integer> {
 	private Long downstreamBound = null;
 	@Option(names = {"-m", "--match-strand"}, description = "only check peaks with strand matching reference" )
 	private boolean matchStrand = false;
-	@Option(names = {"-z", "--compression"}, description = "Output compressed GFF file" )
+	@Option(names = {"-z", "--gzip"}, description = "gzip output (default=false)" )
 	private boolean gzOutput = false;
 	@Option(names = {"--gff"}, description = "input is GFF format (default=BED format)")
 	private boolean isGFF = false;

src/main/java/scriptmanager/cli/Read_Analysis/TransposeMatrixCLI.java

@@ -34,7 +34,7 @@ public class TransposeMatrixCLI implements Callable<Integer> {
 	private int startROW = 0;
 	@Option(names = {"-l", "--start-col"}, description = "Column to start transposing the matrix (zero indexed)")
 	private int startCOL = 0;
-	@Option(names = {"-z", "--compression"}, description = "Output compressed file" )
+	@Option(names = { "-z", "--gzip" }, description = "gzip output (default=false)")
 	private boolean gzOutput = false;
 
 

src/main/java/scriptmanager/window_interface/Sequence_Analysis/RandomizeFASTAWindow.java

@@ -203,7 +203,6 @@ public void actionPerformed(ActionEvent arg0) {
 		chckbxGzipOutput = new JCheckBox("Output GZip");
 		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxGzipOutput, 0, SpringLayout.NORTH, btnCalculate);
 		sl_contentPane.putConstraint(SpringLayout.WEST, chckbxGzipOutput, 30, SpringLayout.WEST, contentPane);
-		chckbxGzipOutput.setEnabled(false);
 		contentPane.add(chckbxGzipOutput);
 
 		progressBar = new JProgressBar();