Mercurial > repos > jtilman > flexbar

changeset 12:4cbf6c6d2f2b

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Fixed issue where adapter removal can not be performed and further minor issues.
author jtilman
date Thu, 17 Jan 2013 18:09:44 +0100
parents 52c5e53aff28
children 346a2b0979ea
files flexbar.pl flexbar.xml
diffstat 2 files changed, 5 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- 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 = $_;
--- 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