Do not decode \r and \n in gff attributes

CHANGELOG.md

@@ -1,3 +1,9 @@
+New in 1.18.1
+=============
+
+* `print` command does not decode the URL escapes for line feed and carriage
+  return. Decoding `\n` and `\r` would split a gff line when printed.
+
 New in 1.18.0
 =============
 

src/main/java/samTextViewer/ArgParse.java

@@ -11,7 +11,7 @@
 public class ArgParse {
 
     public static String PROG_NAME= "ASCIIGenome";
-    public static String VERSION= "1.18.0";
+    public static String VERSION= "1.18.1";
     public static String WEB_ADDRESS= "https://github.com/dariober/ASCIIGenome";
     public static String WEB_RTD= "http://asciigenome.readthedocs.io/";
 

src/main/java/tracks/Track.java

@@ -477,6 +477,8 @@ public String printLines() throws InvalidGenomicCoordsException, IOException, In
                     String field = lst.get(i);
                     if(i == 8) {
                         field = java.net.URLDecoder.decode(field, StandardCharsets.UTF_8.name());
+                        field = field.replace("\n", "%0A");
+                        field = field.replace("\r", "%0D");
                     }
                     decoded.add(field);
                 }

src/test/java/tracks/TrackTest.java

@@ -254,7 +254,6 @@ public void canHighlightFormatInVcfLines() throws ClassNotFoundException, IOExce
 
     @Test
     public void canParsePrintableLinesWithNoFeatures() throws ClassNotFoundException, IOException, InvalidGenomicCoordsException, InvalidRecordException, SQLException, InvalidColourException, InvalidCommandLineException{
-
         // Test region with no features
         GenomicCoords gc = new GenomicCoords("chr10:1-100000", 80, null, null);
         TrackIntervalFeature tif = new TrackIntervalFeature("test_data/hg19_genes_head.gtf", gc);
@@ -264,6 +263,15 @@ public void canParsePrintableLinesWithNoFeatures() throws ClassNotFoundException
         assertEquals("", tif.printLines());
     }
 
+    @Test
+    public void canPrintLinesWithLineFeedInAttribute() throws ClassNotFoundException, IOException, InvalidGenomicCoordsException, InvalidRecordException, SQLException, InvalidColourException, InvalidCommandLineException{
+        GenomicCoords gc = new GenomicCoords("SM_V7_3:36857637-36858016", 80, null, null);
+        TrackIntervalFeature tif = new TrackIntervalFeature("test_data/newlines.gff", gc);
+        tif.setNoFormat(true);
+        tif.setPrintMode(PrintRawLine.FULL);
+        assertTrue(tif.printLines().contains("InterPro %0Daccession:IPR000980 %0Adescription:SH2 \\ndomain %0Amethod:InterPro"));
+    }
+
     @Test
     public void canParsePrintBAM() throws InvalidGenomicCoordsException, IOException, InvalidColourException, InvalidCommandLineException, ClassNotFoundException, InvalidRecordException, SQLException, InvalidConfigException{
         new Config(null);

test_data/newlines.gff

@@ -0,0 +1,2 @@
+# Gene gene:Smp_000640
+SM_V7_3	WormBase_imported	gene	36857637	36863561	.	+	.	ID=transcript:Smp_000640.2;info=method:InterPro %0Daccession:IPR000980 %0Adescription:SH2 \ndomain %0Amethod:InterPro