[med-svn] [giira] 08/09: Adapt patches

[Andreas Tille]

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tille pushed a commit to branch master
in repository giira.

commit 692c173f93a2aaf70c1b1b97335b43d60145cc59
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jan 9 12:04:25 2017 +0100

    Adapt patches
---
 debian/patches/fix_non-ascii_characters.patch | 15 ---------------
 debian/patches/fix_scripts-path.patch         | 12 ++++++------
 debian/patches/remove_cplex_code.patch        |  6 +++---
 debian/patches/series                         |  1 -
 debian/rules                                  |  1 +
 5 files changed, 10 insertions(+), 25 deletions(-)

diff --git a/debian/patches/fix_non-ascii_characters.patch b/debian/patches/fix_non-ascii_characters.patch
deleted file mode 100644
index 400d034..0000000
--- a/debian/patches/fix_non-ascii_characters.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Updated: Sat, 08 Feb 2014 14:38:38 +0100
-Description: Remove non-ASII character from comment
-
---- a/src/types/Rna.java
-+++ b/src/types/Rna.java
-@@ -17,7 +17,7 @@ public class Rna {
- 	
- 	public double quality; 	  	
- 
--	public Vector<Object[]> contigsMappedOn = new Vector<Object[]>(); // contains several Arrays á: [contig, alignPos, cigarString, mapQual,spliceInfo,mismatchInfo,direcInfo] (one for each hit)
-+	public Vector<Object[]> contigsMappedOn = new Vector<Object[]>(); // contains several Arrays: [contig, alignPos, cigarString, mapQual,spliceInfo,mismatchInfo,direcInfo] (one for each hit)
- 	
- 	public int isMulti;		// indicator if this read is an ambiguous read
- 	
diff --git a/debian/patches/fix_scripts-path.patch b/debian/patches/fix_scripts-path.patch
index c0ea1ca..940929e 100644
--- a/debian/patches/fix_scripts-path.patch
+++ b/debian/patches/fix_scripts-path.patch
@@ -14,7 +14,7 @@ Description: Hardcode path to Python helper scripts
 
 --- a/src/geneFinder/ReadInParameters_GeneFinder.java
 +++ b/src/geneFinder/ReadInParameters_GeneFinder.java
-@@ -357,7 +357,7 @@ public class ReadInParameters_GeneFinder
+@@ -379,7 +379,7 @@ public class ReadInParameters_GeneFinder
  			try {
  				String decodedPath = URLDecoder.decode(path, "UTF-8");
  				String scriptPath = decodedPath.substring(0,decodedPath.length()-9);
@@ -25,12 +25,12 @@ Description: Hardcode path to Python helper scripts
  			}
 --- a/src/geneFinder/Giira.java
 +++ b/src/geneFinder/Giira.java
-@@ -43,7 +43,7 @@ public class Giira {
- 		
- 		try {
+@@ -45,7 +45,7 @@ public class Giira {
  			String decodedPath = URLDecoder.decode(path, "UTF-8");
--			String scriptPath = decodedPath.substring(0,decodedPath.length()-9);
+ 			String[] pathArr = decodedPath.split("/");
+ 			int lengthName = pathArr[pathArr.length-1].length();
+-			String scriptPath = decodedPath.substring(0,decodedPath.length()-lengthName);
 +			String scriptPath = "/usr/share/giira/";
+ 			//String scriptPath = decodedPath.substring(0,decodedPath.length()-9);
  			//System.out.println("Path of Giira: " + decodedPath);
  			
- 			classPath = "";
diff --git a/debian/patches/remove_cplex_code.patch b/debian/patches/remove_cplex_code.patch
index d7821df..cfddf19 100644
--- a/debian/patches/remove_cplex_code.patch
+++ b/debian/patches/remove_cplex_code.patch
@@ -8,7 +8,7 @@ Last-Updated: 2014-02-08
 Forwarded: no
 --- a/src/geneFinder/ReadInParameters_GeneFinder.java
 +++ b/src/geneFinder/ReadInParameters_GeneFinder.java
-@@ -242,9 +242,8 @@ public class ReadInParameters_GeneFinder
+@@ -249,9 +249,8 @@ public class ReadInParameters_GeneFinder
  						GeneFinder.useGLPK = true;
  						inputText += "Using glpk for ambiguous read optimization.\n";
  					} else{
@@ -20,7 +20,7 @@ Forwarded: no
  					}
  				} else if(arg.equals("-mem")){
  					GeneFinder.memForCplex = Integer.parseInt(args[i+1]);			
-@@ -376,7 +375,8 @@ public class ReadInParameters_GeneFinder
+@@ -398,7 +397,8 @@ public class ReadInParameters_GeneFinder
  			GeneFinder.noAmbiOpti = false;
  		}
  		if(!foundOptiMethod){
@@ -30,7 +30,7 @@ Forwarded: no
  		}
  		if(!foundSolveOn){
  			GeneFinder.optiSolve = true;
-@@ -462,8 +462,6 @@ public class ReadInParameters_GeneFinder
+@@ -545,8 +545,6 @@ public class ReadInParameters_GeneFinder
  				" \n -haveSam [samfileName]: if a sam file already exists, provide the name, else a mapping is performed. NOTE: the sam file has to be sorted according to read names! \n" +
  				" \n -nT [numberThreads] : specify the maximal number of threads that are allowed to be used, DEFAULT: 1 \n" +
  				" \n -mT [tophat/bwa/bwasw] : specify desired tool for the read mapping, DEFAULT: tophat \n" +
diff --git a/debian/patches/series b/debian/patches/series
index 2eb66d5..6222007 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,2 @@
 remove_cplex_code.patch
-fix_non-ascii_characters.patch
 fix_scripts-path.patch
diff --git a/debian/rules b/debian/rules
index 387628d..3585591 100755
--- a/debian/rules
+++ b/debian/rules
@@ -5,6 +5,7 @@
 SRC_VERSION =$(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p')
 
 export JAVA_HOME=/usr/lib/jvm/default-java
+export LC_ALL=C.UTF-8
 
 %:
 	dh $@ --with javahelper

-- 
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