Subject: load config in /etc
Description: use config in Debian etc dirs instead of embedding data in jar
Author: Olivier Sallou <osallou@debian.org>
Last-Updated: 2014-08-19
Forwarded: no

--- 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;
 import java.io.InputStream;
+import java.io.FileInputStream;
 import java.io.InputStreamReader;
 import java.util.HashMap;
 
@@ -82,7 +83,7 @@ public class ModuleConfig {
 		
 		try {
 			if (FastQCConfig.getInstance().limits_file == null) {
-				InputStream rsrc=ContaminentFinder.class.getResourceAsStream("/Configuration/limits.txt");
+				InputStream rsrc = new FileInputStream("/etc/fastqc/Configuration/limits.txt");
 				if (rsrc==null) throw new FileNotFoundException("cannot find Configuration/limits.txt");
 				br =new BufferedReader(new InputStreamReader(rsrc));
 			}
--- 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;
 
@@ -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");
+				// 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");
 				br =new BufferedReader(new InputStreamReader(rsrc));
 			}
--- 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;
 import java.io.InputStream;
+import java.io.FileInputStream;
 import java.io.InputStreamReader;
 import java.util.Vector;
 
@@ -65,8 +66,8 @@ public class ContaminentFinder {
 			
 			BufferedReader br = null;
 			if (FastQCConfig.getInstance().contaminant_file == null) {
-				InputStream rsrc=ContaminentFinder.class.getResourceAsStream("/Configuration/contaminant_list.txt");
-				if (rsrc==null) throw new FileNotFoundException("cannot find Confituration/contaminant_list.txt");
+				InputStream rsrc = new FileInputStream("/etc/fastqc/Configuration/contaminant_list.txt");
+				if (rsrc==null) throw new FileNotFoundException("cannot find /etc/fastqc/Configuration/contaminant_list.txt");
 				br =new BufferedReader(new InputStreamReader(rsrc));
 			}
 			else {