[med-svn] [fastqc] 01/03: Adapt patches to new upstream version

[Andreas Tille]

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tille pushed a commit to branch master
in repository fastqc.

commit e708ae26924954292e44695d5d1cb877c9e7c53c
Author: Andreas Tille <tille at debian.org>
Date:   Sun May 3 08:44:25 2015 +0200

    Adapt patches to new upstream version
---
 debian/patches/series                              |  2 +-
 ...iguration_path => set_configuration_path.patch} | 31 +++++++++-------------
 2 files changed, 13 insertions(+), 20 deletions(-)

diff --git a/debian/patches/series b/debian/patches/series
index c8c3ad6..ee6c7d1 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,4 @@
 Makefile.patch
 fastqc.patch
 fix-help-call.patch
-set_configuration_path
+set_configuration_path.patch
diff --git a/debian/patches/set_configuration_path b/debian/patches/set_configuration_path.patch
similarity index 66%
rename from debian/patches/set_configuration_path
rename to debian/patches/set_configuration_path.patch
index 5758be2..d5d3e67 100644
--- a/debian/patches/set_configuration_path
+++ b/debian/patches/set_configuration_path.patch
@@ -3,10 +3,9 @@ Description: use config in Debian etc dirs instead of embedding data in jar
 Author: Olivier Sallou <osallou at debian.org>
 Last-Updated: 2014-08-19
 Forwarded: no
-Index: FastQC/uk/ac/babraham/FastQC/Modules/ModuleConfig.java
-===================================================================
---- FastQC.orig/uk/ac/babraham/FastQC/Modules/ModuleConfig.java
-+++ FastQC/uk/ac/babraham/FastQC/Modules/ModuleConfig.java
+
+--- a/uk/ac/babraham/FastQC/Modules/ModuleConfig.java
++++ b/uk/ac/babraham/FastQC/Modules/ModuleConfig.java
 @@ -23,6 +23,7 @@ import java.io.BufferedReader;
  import java.io.FileNotFoundException;
  import java.io.FileReader;
@@ -25,34 +24,28 @@ Index: FastQC/uk/ac/babraham/FastQC/Modules/ModuleConfig.java
  				if (rsrc==null) throw new FileNotFoundException("cannot find Configuration/limits.txt");
  				br =new BufferedReader(new InputStreamReader(rsrc));
  			}
-Index: FastQC/uk/ac/babraham/FastQC/Modules/AdapterContent.java
-===================================================================
---- FastQC.orig/uk/ac/babraham/FastQC/Modules/AdapterContent.java
-+++ FastQC/uk/ac/babraham/FastQC/Modules/AdapterContent.java
-@@ -27,6 +27,7 @@ import java.io.FileNotFoundException;
+--- a/uk/ac/babraham/FastQC/Modules/AdapterContent.java
++++ b/uk/ac/babraham/FastQC/Modules/AdapterContent.java
+@@ -25,6 +25,7 @@ import java.io.FileNotFoundException;
  import java.io.FileReader;
  import java.io.IOException;
  import java.io.InputStream;
 +import java.io.FileInputStream;
  import java.io.InputStreamReader;
  import java.util.Vector;
- import java.util.zip.ZipEntry;
-@@ -75,8 +76,9 @@ public class AdapterContent extends Abst
+ 
+@@ -70,7 +71,8 @@ public class AdapterContent extends Abst
  
  			BufferedReader br = null;
  			if (FastQCConfig.getInstance().adapter_file == null) {
 -				InputStream rsrc=ContaminentFinder.class.getResourceAsStream("/Configuration/adapter_list.txt");
--				if (rsrc==null) throw new FileNotFoundException("cannot find Confituration/adapter_list.txt");
-+				//InputStream rsrc=ContaminentFinder.class.getResourceAsStream("/usr/share/fastqc/Configuration/adapter_list.txt");
++				// InputStream rsrc=ContaminentFinder.class.getResourceAsStream("/Configuration/adapter_list.txt");
 +				InputStream rsrc = new FileInputStream("/etc/fastqc/Configuration/adapter_list.txt");
-+				if (rsrc==null) throw new FileNotFoundException("cannot find Configuration/adapter_list.txt");
+ 				if (rsrc==null) throw new FileNotFoundException("cannot find Configuration/adapter_list.txt");
  				br =new BufferedReader(new InputStreamReader(rsrc));
  			}
- 			else {
-Index: FastQC/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.java
-===================================================================
---- FastQC.orig/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.java
-+++ FastQC/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.java
+--- a/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.java
++++ b/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.java
 @@ -24,6 +24,7 @@ import java.io.FileNotFoundException;
  import java.io.FileReader;
  import java.io.IOException;

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