# HG changeset patch
# User jtilman
# Date 1358442584 -3600
# Node ID 4cbf6c6d2f2b71c9c4ca02e25457f1132c9126f9
# Parent  52c5e53aff28d7b952d534d2b3609f3689f552fc
Fixed issue where adapter removal can not be performed and further minor issues.

diff -r 52c5e53aff28 -r 4cbf6c6d2f2b flexbar.pl
--- a/flexbar.pl	Wed Jan 02 12:54:28 2013 +0100
+++ b/flexbar.pl	Thu Jan 17 18:09:44 2013 +0100
@@ -18,7 +18,7 @@
 	my $fileType;
 	
 	$fileType = $1         if /\.(\w+)$/;
-	$fileType = $format    if /\.\w+fast\w$/;
+	$fileType = $format    if /\.\w*fast\w$/;
 	$fileType = 'tabular'  if $fileType eq 'lengthdist';
 	
 	my $file = $_;
diff -r 52c5e53aff28 -r 4cbf6c6d2f2b flexbar.xml
--- a/flexbar.xml	Wed Jan 02 12:54:28 2013 +0100
+++ b/flexbar.xml	Thu Jan 17 18:09:44 2013 +0100
@@ -94,11 +94,10 @@
 				--barcode-mismatch $bMismatch
 				--barcode-gap      $bGap
 			#end if
-			
 		#end if
 		
 		
-		#if $cAdapters.select == "yes":
+		#if $cAdapters.select == "on":
 			
 			#if $cAdapters.ccAdapters.select == "data":
 				--adapters $cAdapters.ccAdapters.adaptersData
@@ -117,22 +116,21 @@
 			--adapter-min-overlap $cAdapters.aMinOverlap
 			--adapter-threshold   $cAdapters.aThresh
 			
-			#if $cAdapters.caAlignScores.select == "on":
+			#if $cAdapters.caAlignScores.select == "yes":
 				--adapter-match    $aMatch
 				--adapter-mismatch $aMismatch
 				--adapter-gap      $aGap
 			#end if
-			
 		#end if
 		
 		
-		#if $cLogging.select == "show"
+		#if $cLogging.select == "show":
 			$cLogging.logLevel
 			$cLogging.noLenDist
 			$cLogging.remTag
 		#end if
 		
-		#if $cLogging.select == "off"
+		#if $cLogging.select == "off":
 			--no-length-dist
 		#end if