[med-svn] [trimmomatic] 01/01: Corrected patch for trimmomatic

[Steffen Möller]

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moeller pushed a commit to branch master
in repository trimmomatic.

commit fdac1374c8f0550ff5bac6ec38b5348e73d96569
Author: Steffen Moeller <moeller at debian.org>
Date:   Wed Mar 2 21:18:14 2016 +0100

    Corrected patch for trimmomatic
---
 .../patches/search_in_usr_share_trimmomatic.patch  | 26 ++++++++++++----------
 1 file changed, 14 insertions(+), 12 deletions(-)

diff --git a/debian/patches/search_in_usr_share_trimmomatic.patch b/debian/patches/search_in_usr_share_trimmomatic.patch
index 272ad80..4a50d58 100644
--- a/debian/patches/search_in_usr_share_trimmomatic.patch
+++ b/debian/patches/search_in_usr_share_trimmomatic.patch
@@ -2,23 +2,25 @@ Index: trimmomatic/src/org/usadellab/trimmomatic/trim/IlluminaClippingTrimmer.ja
 ===================================================================
 --- trimmomatic.orig/src/org/usadellab/trimmomatic/trim/IlluminaClippingTrimmer.java
 +++ trimmomatic/src/org/usadellab/trimmomatic/trim/IlluminaClippingTrimmer.java
-@@ -49,7 +49,18 @@ public class IlluminaClippingTrimmer imp
+@@ -49,7 +49,20 @@ public class IlluminaClippingTrimmer imp
  	{
  		String arg[] = args.split(":");
  		
 -		File seqs=new File(arg[0]);
-+		File seqs;
-+		if (File.exists(arg[0])) {
-+			seqs = new File(arg[0]);
++		File seqs = new File(arg[0]);
++		if (!seqs.exists()) {
++			if ( (!arg[0].startsWith("/")) && (!arg[0].startsWith(".."))) {
++				seqs = new File("/usr/share/trimmomatic/"+arg[0]);
++				if (!seqs.exists()) {
++					System.err.println("E: Could not find '"+arg[0]+"' in local directory or /usr/share/trimmomatic.");
++					System.exit(1);
++				}
++			}
++			else if (!seqs.exists()) {
++				System.err.println("E: Could not find '"+arg[0]+"'.");
++				System.exit(1);
++			}
 +		}
-+		else if (!arg[0].startsWith("/") and !arg[0].startsWith("..") and File.exists("/usr/share/trimmomatic/"+arg[0])) {
-+			seqs = new File("/usr/share/trimmomatic/"+arg[0]);
-+		}
-+		else {
-+			System.err.println("E: Could not find '"+arg[0]+"' in local directory or /usr/share/trimmomatic.")
-+			System.exit(1);
-+		}
-+
  
  		int seedMaxMiss = Integer.parseInt(arg[1]);
  		int minPalindromeLikelihood = Integer.parseInt(arg[2]);

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