[med-svn] [fastqc] 05/06: Adapt patches
Andreas Tille
tille at debian.org
Sun Mar 20 13:46:00 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository fastqc.
commit 3c67afd49824a939f44de7ca7ae48de47551fd0f
Author: Andreas Tille <tille at debian.org>
Date: Sun Mar 20 14:27:37 2016 +0100
Adapt patches
---
debian/changelog | 4 +-
debian/patches/adapt_to_htslib.patch | 54 +++++++--------
debian/patches/fix-help-call.patch | 16 ++---
debian/patches/set_configuration_path.patch | 103 ++++++++++++++--------------
4 files changed, 89 insertions(+), 88 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 8ef7d84..308646c 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-fastqc (0.11.5+dfsg-1) UNRELEASED; urgency=medium
+fastqc (0.11.5+dfsg-1) unstable; urgency=medium
[ Steffen Moeller ]
* Contribued EDAM ontology description to
@@ -8,7 +8,7 @@ fastqc (0.11.5+dfsg-1) UNRELEASED; urgency=medium
* New upstream version
* Add compression method to watch file
- -- Andreas Tille <tille at debian.org> Sun, 20 Mar 2016 14:06:29 +0100
+ -- Andreas Tille <tille at debian.org> Sun, 20 Mar 2016 14:08:48 +0100
fastqc (0.11.4+dfsg-3) unstable; urgency=medium
diff --git a/debian/patches/adapt_to_htslib.patch b/debian/patches/adapt_to_htslib.patch
index be269ac..a2ea9ae 100644
--- a/debian/patches/adapt_to_htslib.patch
+++ b/debian/patches/adapt_to_htslib.patch
@@ -6,30 +6,30 @@ Description: Path to samtools changed when switching from libsam-java
--- a/uk/ac/babraham/FastQC/Sequence/BAMFile.java
+++ b/uk/ac/babraham/FastQC/Sequence/BAMFile.java
-@@ -25,11 +25,12 @@
- import java.util.Iterator;
- import java.util.List;
-
--import net.sf.samtools.CigarElement;
--import net.sf.samtools.CigarOperator;
--import net.sf.samtools.SAMFileReader;
--import net.sf.samtools.SAMFormatException;
--import net.sf.samtools.SAMRecord;
-+import htsjdk.samtools.CigarElement;
-+import htsjdk.samtools.CigarOperator;
-+import htsjdk.samtools.SAMFileReader;
-+import htsjdk.samtools.SAMFormatException;
-+import htsjdk.samtools.SAMRecord;
-+import htsjdk.samtools.ValidationStringency;
-
- public class BAMFile implements SequenceFile {
-
-@@ -55,7 +56,7 @@
- name = file.getName();
- this.onlyMapped = onlyMapped;
-
-- SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.SILENT);
-+ SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
-
- fis = new FileInputStream(file);
-
+@@ -25,11 +25,12 @@ import java.io.IOException;
+ import java.util.Iterator;
+ import java.util.List;
+
+-import net.sf.samtools.CigarElement;
+-import net.sf.samtools.CigarOperator;
+-import net.sf.samtools.SAMFileReader;
+-import net.sf.samtools.SAMFormatException;
+-import net.sf.samtools.SAMRecord;
++import htsjdk.samtools.CigarElement;
++import htsjdk.samtools.CigarOperator;
++import htsjdk.samtools.SAMFileReader;
++import htsjdk.samtools.SAMFormatException;
++import htsjdk.samtools.SAMRecord;
++import htsjdk.samtools.ValidationStringency;
+
+ public class BAMFile implements SequenceFile {
+
+@@ -55,7 +56,7 @@ public class BAMFile implements Sequence
+ name = file.getName();
+ this.onlyMapped = onlyMapped;
+
+- SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.SILENT);
++ SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
+
+ fis = new FileInputStream(file);
+
diff --git a/debian/patches/fix-help-call.patch b/debian/patches/fix-help-call.patch
index 353b553..175bbd4 100644
--- a/debian/patches/fix-help-call.patch
+++ b/debian/patches/fix-help-call.patch
@@ -8,11 +8,11 @@ Subject: The original way to open Help text ends up in an exception
--- a/uk/ac/babraham/FastQC/FastQCMenuBar.java
+++ b/uk/ac/babraham/FastQC/FastQCMenuBar.java
@@ -132,7 +132,7 @@ public class FastQCMenuBar extends JMenu
- }
- else if (command.equals("help_contents")) {
- try {
-- new HelpDialog(application,new File(URLDecoder.decode(ClassLoader.getSystemResource("Help").getFile(),"UTF-8")));
-+ new HelpDialog(application,new File(URLDecoder.decode("/usr/share/fastqc/Help","UTF-8")));
- }
- catch (UnsupportedEncodingException e1) {
- e1.printStackTrace();
+ }
+ else if (command.equals("help_contents")) {
+ try {
+- new HelpDialog(application,new File(URLDecoder.decode(ClassLoader.getSystemResource("Help").getFile(),"UTF-8")));
++ new HelpDialog(application,new File(URLDecoder.decode("/usr/share/fastqc/Help","UTF-8")));
+ }
+ catch (UnsupportedEncodingException e1) {
+ e1.printStackTrace();
diff --git a/debian/patches/set_configuration_path.patch b/debian/patches/set_configuration_path.patch
index d5d3e67..8fc0c9c 100644
--- a/debian/patches/set_configuration_path.patch
+++ b/debian/patches/set_configuration_path.patch
@@ -7,62 +7,63 @@ 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;
-
+ 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 +83,8 @@ public class ModuleConfig {
-
- try {
- if (FastQCConfig.getInstance().limits_file == null) {
-- InputStream rsrc=ContaminentFinder.class.getResourceAsStream("/Configuration/limits.txt");
-+ //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));
- }
+
+ try {
+ if (FastQCConfig.getInstance().limits_file == null) {
+- InputStream rsrc=ContaminentFinder.class.getResourceAsStream("/Configuration/limits.txt");
++ //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;
-
+ 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));
- }
+
+ 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 +66,9 @@ 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=ContaminentFinder.class.getResourceAsStream("/Configuration/contaminant_list.txt");
-+ InputStream rsrc = new FileInputStream("/etc/fastqc/Configuration/contaminant_list.txt");
-+ if (rsrc==null) throw new FileNotFoundException("cannot find Configuration/contaminant_list.txt");
- br =new BufferedReader(new InputStreamReader(rsrc));
- }
- else {
+ 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 +66,10 @@ 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=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 Configuration/contaminant_list.txt");
+ br =new BufferedReader(new InputStreamReader(rsrc));
+ }
+ else {
--
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