updated doc to reflect the code change

.classpath

 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
+	<classpathentry including="**/*.java" kind="src" output="target/classes" path="src/main/java">
 		<attributes>
 			<attribute name="optional" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
@@ -27,7 +27,7 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.launching.macosx.MacOSXType/Java 1.7.0">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>

.gitignore

@@ -4,3 +4,4 @@ bin
 target/
 .DS_Store
 ._*
+embl.properties

src/main/java/org/embl/gbcs/je/jemultiplexer/AbstractJemultiplexer.java

@@ -173,7 +173,8 @@ public abstract class AbstractJemultiplexer extends CommandLineProgram {
 					+" When true and if only one of the two reads has a barcode match, the read pair is 'unassigned'.\n"
 					+" When false and if only one of the two reads has a barcode match, the read pair is assigned to the\n"
 					+" corresponding sample\n"
-					+ "When reads resolve to different samples, the read pair is always 'unassigned'.\n"
+					+ "When false and reads resolve to different samples, the read pair with the lowest mismatch is chosen\n "
+					+ "(read pair is 'unassigned' in case of mismatch equality).\n"
 			)
 	public boolean STRICT = false;