[med-svn] [artemis] 01/03: fix FTBFS by adjusting API calls

Sascha Steinbiss sascha at steinbiss.name
Fri Mar 25 12:05:03 UTC 2016 

This is an automated email from the git hooks/post-receive script.

sascha-guest pushed a commit to branch master
in repository artemis.

commit cfbf441dce4d89e8a4b9ccf86c1c1115d934cfb4
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Fri Mar 25 11:24:07 2016 +0000

    fix FTBFS by adjusting API calls
---
 debian/changelog                       |   6 ++
 debian/patches/htsjdk-api-change.patch |  13 ++++
 debian/patches/picard-api-change.patch | 115 ++++++++++++++++++---------------
 debian/patches/series                  |   1 +
 4 files changed, 83 insertions(+), 52 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index ea8062a..2c6f5ed 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,6 +3,12 @@ artemis (16.0.0+dfsg-5) UNRELEASED; urgency=medium
   [ Steffen Moeller and Jon Ison ]
   * Introduced EDAM annotation
 
+  [ Sascha Steinbiss ]
+  * Additional work updating APIs
+
+  [ Afif Elghraoui ]
+  * Patch code to match new htsjdk API
+
  -- Afif Elghraoui <afif at ghraoui.name>  Wed, 23 Dec 2015 19:38:33 -0800
 
 artemis (16.0.0+dfsg-4) unstable; urgency=high
diff --git a/debian/patches/htsjdk-api-change.patch b/debian/patches/htsjdk-api-change.patch
new file mode 100644
index 0000000..f05d5ee
--- /dev/null
+++ b/debian/patches/htsjdk-api-change.patch
@@ -0,0 +1,13 @@
+Description: adjust log configuration to new API
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
++++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
+@@ -116,7 +116,7 @@
+ import htsjdk.samtools.SAMReadGroupRecord;
+ import htsjdk.samtools.SAMRecord;
+ import htsjdk.samtools.SAMSequenceRecord;
+-import htsjdk.samtools.SAMFileReader.ValidationStringency;
++import htsjdk.samtools.ValidationStringency;
+ import htsjdk.samtools.util.CloseableIterator;
+ 
+ import uk.ac.sanger.artemis.Entry;
diff --git a/debian/patches/picard-api-change.patch b/debian/patches/picard-api-change.patch
index 94b869b..261033a 100644
--- a/debian/patches/picard-api-change.patch
+++ b/debian/patches/picard-api-change.patch
@@ -2,8 +2,8 @@ Description: Use htsjdk for dropped picard and sam functionality
 Author: Afif Elghraoui <afif at ghraoui.name>
 Forwarded: no
 Last-Update: 2015-12-24
---- artemis.orig/uk/ac/sanger/artemis/io/IndexFastaStream.java
-+++ artemis/uk/ac/sanger/artemis/io/IndexFastaStream.java
+--- a/uk/ac/sanger/artemis/io/IndexFastaStream.java
++++ b/uk/ac/sanger/artemis/io/IndexFastaStream.java
 @@ -30,10 +30,10 @@
  
  import javax.swing.JOptionPane;
@@ -26,8 +26,8 @@ Last-Update: 2015-12-24
 -}
 \ No newline at end of file
 +}
---- artemis.orig/uk/ac/sanger/artemis/components/alignment/CRAMReferenceSequenceFile.java
-+++ artemis/uk/ac/sanger/artemis/components/alignment/CRAMReferenceSequenceFile.java
+--- a/uk/ac/sanger/artemis/components/alignment/CRAMReferenceSequenceFile.java
++++ b/uk/ac/sanger/artemis/components/alignment/CRAMReferenceSequenceFile.java
 @@ -23,9 +23,9 @@
   */
  package uk.ac.sanger.artemis.components.alignment;
@@ -41,8 +41,8 @@ Last-Update: 2015-12-24
  import uk.ac.sanger.artemis.Entry;
  import uk.ac.sanger.artemis.io.Range;
  import uk.ac.sanger.artemis.sequence.Bases;
---- artemis.orig/uk/ac/sanger/artemis/components/alignment/BamView.java
-+++ artemis/uk/ac/sanger/artemis/components/alignment/BamView.java
+--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
++++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
 @@ -107,17 +107,17 @@
  
  import org.apache.log4j.Level;
@@ -72,6 +72,17 @@ Last-Update: 2015-12-24
  
  import uk.ac.sanger.artemis.Entry;
  import uk.ac.sanger.artemis.EntryGroup;
+@@ -525,8 +525,8 @@
+     if(feature_display != null && bam.endsWith("cram"))
+     {
+       // set log level
+-      net.sf.picard.util.Log.setGlobalLogLevel( 
+-          net.sf.picard.util.Log.LogLevel.ERROR);
++      htsjdk.samtools.util.Log.setGlobalLogLevel(
++         htsjdk.samtools.util.Log.LogLevel.ERROR);
+       final CRAMReferenceSequenceFile ref = new CRAMReferenceSequenceFile(
+         feature_display.getEntryGroup().getSequenceEntry(), this);
+       
 @@ -536,7 +536,7 @@
  
        try
@@ -99,8 +110,8 @@ Last-Update: 2015-12-24
          {
            JOptionPane.showMessageDialog(this, re.getMessage());
          }
---- artemis.orig/uk/ac/sanger/artemis/components/alignment/BamUtils.java
-+++ artemis/uk/ac/sanger/artemis/components/alignment/BamUtils.java
+--- a/uk/ac/sanger/artemis/components/alignment/BamUtils.java
++++ b/uk/ac/sanger/artemis/components/alignment/BamUtils.java
 @@ -28,10 +28,10 @@
  import java.util.List;
  import java.util.Vector;
@@ -116,8 +127,8 @@ Last-Update: 2015-12-24
  import uk.ac.sanger.artemis.Feature;
  import uk.ac.sanger.artemis.FeatureSegmentVector;
  import uk.ac.sanger.artemis.io.Range;
---- artemis.orig/uk/ac/sanger/artemis/components/alignment/BamViewRecord.java
-+++ artemis/uk/ac/sanger/artemis/components/alignment/BamViewRecord.java
+--- a/uk/ac/sanger/artemis/components/alignment/BamViewRecord.java
++++ b/uk/ac/sanger/artemis/components/alignment/BamViewRecord.java
 @@ -1,6 +1,6 @@
  package uk.ac.sanger.artemis.components.alignment;
  
@@ -126,8 +137,8 @@ Last-Update: 2015-12-24
  
  
  class BamViewRecord
---- artemis.orig/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
-+++ artemis/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
+--- a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
++++ b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
 @@ -51,8 +51,8 @@
  
  import uk.ac.sanger.artemis.components.Plot;
@@ -139,8 +150,8 @@ Last-Update: 2015-12-24
  
    public class CoveragePanel extends AbstractGraphPanel
    {
---- artemis.orig/uk/ac/sanger/artemis/components/alignment/MappedReads.java
-+++ artemis/uk/ac/sanger/artemis/components/alignment/MappedReads.java
+--- a/uk/ac/sanger/artemis/components/alignment/MappedReads.java
++++ b/uk/ac/sanger/artemis/components/alignment/MappedReads.java
 @@ -37,7 +37,7 @@
  import uk.ac.sanger.artemis.util.OutOfRangeException;
  import uk.ac.sanger.artemis.util.ReadOnlyException;
@@ -150,8 +161,8 @@ Last-Update: 2015-12-24
  
  public class MappedReads
  {
---- artemis.orig/uk/ac/sanger/artemis/components/alignment/PairedReadComparator.java
-+++ artemis/uk/ac/sanger/artemis/components/alignment/PairedReadComparator.java
+--- a/uk/ac/sanger/artemis/components/alignment/PairedReadComparator.java
++++ b/uk/ac/sanger/artemis/components/alignment/PairedReadComparator.java
 @@ -26,7 +26,7 @@
  
  import java.util.Comparator;
@@ -161,8 +172,8 @@ Last-Update: 2015-12-24
  
  import uk.ac.sanger.artemis.components.alignment.BamView.PairedRead;
  
---- artemis.orig/uk/ac/sanger/artemis/components/alignment/ReadGroupsFrame.java
-+++ artemis/uk/ac/sanger/artemis/components/alignment/ReadGroupsFrame.java
+--- a/uk/ac/sanger/artemis/components/alignment/ReadGroupsFrame.java
++++ b/uk/ac/sanger/artemis/components/alignment/ReadGroupsFrame.java
 @@ -24,7 +24,7 @@
  import javax.swing.JScrollPane;
  import javax.swing.SwingUtilities;
@@ -172,8 +183,8 @@ Last-Update: 2015-12-24
  
  class ReadGroupsFrame extends JFrame
  {
---- artemis.orig/uk/ac/sanger/artemis/components/alignment/RunSamTools.java
-+++ artemis/uk/ac/sanger/artemis/components/alignment/RunSamTools.java
+--- a/uk/ac/sanger/artemis/components/alignment/RunSamTools.java
++++ b/uk/ac/sanger/artemis/components/alignment/RunSamTools.java
 @@ -26,7 +26,7 @@
  import java.io.*;
  import java.util.List;
@@ -183,8 +194,8 @@ Last-Update: 2015-12-24
  
  /**
  * Used to run an samtools process this reads stdout and 
---- artemis.orig/uk/ac/sanger/artemis/components/alignment/SAMRecordFlagConjunctionPredicate.java
-+++ artemis/uk/ac/sanger/artemis/components/alignment/SAMRecordFlagConjunctionPredicate.java
+--- a/uk/ac/sanger/artemis/components/alignment/SAMRecordFlagConjunctionPredicate.java
++++ b/uk/ac/sanger/artemis/components/alignment/SAMRecordFlagConjunctionPredicate.java
 @@ -23,7 +23,7 @@
  
  import java.util.Vector;
@@ -194,8 +205,8 @@ Last-Update: 2015-12-24
  
  /**
   *  Test the SAMRecord flag.
---- artemis.orig/uk/ac/sanger/artemis/components/alignment/SAMRecordFlagPredicate.java
-+++ artemis/uk/ac/sanger/artemis/components/alignment/SAMRecordFlagPredicate.java
+--- a/uk/ac/sanger/artemis/components/alignment/SAMRecordFlagPredicate.java
++++ b/uk/ac/sanger/artemis/components/alignment/SAMRecordFlagPredicate.java
 @@ -21,7 +21,7 @@
  
  package uk.ac.sanger.artemis.components.alignment;
@@ -205,8 +216,8 @@ Last-Update: 2015-12-24
  
  /**
   *  Test the SAMRecord flag.
---- artemis.orig/uk/ac/sanger/artemis/components/alignment/SAMRecordList.java
-+++ artemis/uk/ac/sanger/artemis/components/alignment/SAMRecordList.java
+--- a/uk/ac/sanger/artemis/components/alignment/SAMRecordList.java
++++ b/uk/ac/sanger/artemis/components/alignment/SAMRecordList.java
 @@ -53,7 +53,7 @@
  import uk.ac.sanger.artemis.components.alignment.BamViewRecord;
  
@@ -216,8 +227,8 @@ Last-Update: 2015-12-24
  
  public class SAMRecordList extends JPanel
                             implements DisplayAdjustmentListener
---- artemis.orig/uk/ac/sanger/artemis/components/alignment/SAMRecordMapQPredicate.java
-+++ artemis/uk/ac/sanger/artemis/components/alignment/SAMRecordMapQPredicate.java
+--- a/uk/ac/sanger/artemis/components/alignment/SAMRecordMapQPredicate.java
++++ b/uk/ac/sanger/artemis/components/alignment/SAMRecordMapQPredicate.java
 @@ -21,7 +21,7 @@
  
  package uk.ac.sanger.artemis.components.alignment;
@@ -227,8 +238,8 @@ Last-Update: 2015-12-24
  
  /**
   *  Test the SAMRecord mapping quality - mapq flag.
---- artemis.orig/uk/ac/sanger/artemis/components/alignment/SAMRecordPositionComparator.java
-+++ artemis/uk/ac/sanger/artemis/components/alignment/SAMRecordPositionComparator.java
+--- a/uk/ac/sanger/artemis/components/alignment/SAMRecordPositionComparator.java
++++ b/uk/ac/sanger/artemis/components/alignment/SAMRecordPositionComparator.java
 @@ -26,7 +26,7 @@
  
  import java.util.Comparator;
@@ -238,8 +249,8 @@ Last-Update: 2015-12-24
  import uk.ac.sanger.artemis.components.alignment.BamViewRecord;
  
   class SAMRecordPositionComparator implements Comparator<Object>
---- artemis.orig/uk/ac/sanger/artemis/components/alignment/SAMRecordPredicate.java
-+++ artemis/uk/ac/sanger/artemis/components/alignment/SAMRecordPredicate.java
+--- a/uk/ac/sanger/artemis/components/alignment/SAMRecordPredicate.java
++++ b/uk/ac/sanger/artemis/components/alignment/SAMRecordPredicate.java
 @@ -21,7 +21,7 @@
  
  package uk.ac.sanger.artemis.components.alignment;
@@ -249,8 +260,8 @@ Last-Update: 2015-12-24
  
  /**
   *  Each object that implements this interface represents a predicate that can
---- artemis.orig/uk/ac/sanger/artemis/components/alignment/SnpPanel.java
-+++ artemis/uk/ac/sanger/artemis/components/alignment/SnpPanel.java
+--- a/uk/ac/sanger/artemis/components/alignment/SnpPanel.java
++++ b/uk/ac/sanger/artemis/components/alignment/SnpPanel.java
 @@ -42,8 +42,8 @@
  import uk.ac.sanger.artemis.sequence.Bases;
  import uk.ac.sanger.artemis.util.OutOfRangeException;
@@ -262,8 +273,8 @@ Last-Update: 2015-12-24
  
    public class SnpPanel extends AbstractGraphPanel
    {
---- artemis.orig/uk/ac/sanger/artemis/components/variant/BCFReader.java
-+++ artemis/uk/ac/sanger/artemis/components/variant/BCFReader.java
+--- a/uk/ac/sanger/artemis/components/variant/BCFReader.java
++++ b/uk/ac/sanger/artemis/components/variant/BCFReader.java
 @@ -34,7 +34,7 @@
  
  import uk.ac.sanger.artemis.util.FTPSeekableStream;
@@ -273,8 +284,8 @@ Last-Update: 2015-12-24
  
  class BCFReader extends AbstractVCFReader
  {
---- artemis.orig/uk/ac/sanger/artemis/components/variant/IOUtils.java
-+++ artemis/uk/ac/sanger/artemis/components/variant/IOUtils.java
+--- a/uk/ac/sanger/artemis/components/variant/IOUtils.java
++++ b/uk/ac/sanger/artemis/components/variant/IOUtils.java
 @@ -75,7 +75,7 @@
  import uk.ac.sanger.artemis.util.ReadOnlyException;
  import uk.ac.sanger.artemis.util.RemoteFileDocument;
@@ -284,8 +295,8 @@ Last-Update: 2015-12-24
  
  class IOUtils
  { 
---- artemis.orig/uk/ac/sanger/artemis/components/variant/TabixReader.java
-+++ artemis/uk/ac/sanger/artemis/components/variant/TabixReader.java
+--- a/uk/ac/sanger/artemis/components/variant/TabixReader.java
++++ b/uk/ac/sanger/artemis/components/variant/TabixReader.java
 @@ -27,8 +27,8 @@
  
  /* Contact: Heng Li <hengli at broadinstitute.org> */
@@ -297,8 +308,8 @@ Last-Update: 2015-12-24
  
  import java.io.*;
  import java.net.URL;
---- artemis.orig/uk/ac/sanger/artemis/components/variant/VCFview.java
-+++ artemis/uk/ac/sanger/artemis/components/variant/VCFview.java
+--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
++++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
 @@ -86,7 +86,7 @@
  import javax.swing.border.Border;
  import javax.swing.border.EmptyBorder;
@@ -308,8 +319,8 @@ Last-Update: 2015-12-24
  
  import org.apache.log4j.Level;
  
---- artemis.orig/uk/ac/sanger/artemis/io/DocumentEntryFactory.java
-+++ artemis/uk/ac/sanger/artemis/io/DocumentEntryFactory.java
+--- a/uk/ac/sanger/artemis/io/DocumentEntryFactory.java
++++ b/uk/ac/sanger/artemis/io/DocumentEntryFactory.java
 @@ -76,7 +76,7 @@
        throws IOException, EntryInformationException 
    {
@@ -319,8 +330,8 @@ Last-Update: 2015-12-24
      {
        if(IndexedGFFDocumentEntry.isIndexed( ((File)document.getLocation()) ))
          return new IndexedGFFDocumentEntry(document);
---- artemis.orig/uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java
-+++ artemis/uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java
+--- a/uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java
++++ b/uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java
 @@ -38,7 +38,7 @@
  import java.util.Set;
  import java.util.Vector;
@@ -330,8 +341,8 @@ Last-Update: 2015-12-24
  
  import uk.ac.sanger.artemis.EntryGroup;
  import uk.ac.sanger.artemis.components.FeatureDisplay;
---- artemis.orig/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
-+++ artemis/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
+--- a/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
++++ b/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
 @@ -45,7 +45,7 @@
  import javax.swing.JOptionPane;
  import javax.swing.JPanel;
@@ -341,8 +352,8 @@ Last-Update: 2015-12-24
  
  /**
   *  Objects of this class have one useful method - getValues (), which takes a
---- artemis.orig/uk/ac/sanger/artemis/util/FTPSeekableStream.java
-+++ artemis/uk/ac/sanger/artemis/util/FTPSeekableStream.java
+--- a/uk/ac/sanger/artemis/util/FTPSeekableStream.java
++++ b/uk/ac/sanger/artemis/util/FTPSeekableStream.java
 @@ -15,7 +15,7 @@
  import org.apache.commons.net.ftp.FTPReply;
  import org.apache.log4j.Logger;
@@ -352,8 +363,8 @@ Last-Update: 2015-12-24
  
  /**
   * Written independently to, but bugfixed by looking at the Savant
---- artemis.orig/uk/ac/sanger/artemis/util/FileDocument.java
-+++ artemis/uk/ac/sanger/artemis/util/FileDocument.java
+--- a/uk/ac/sanger/artemis/util/FileDocument.java
++++ b/uk/ac/sanger/artemis/util/FileDocument.java
 @@ -166,11 +166,11 @@
  {
    protected static boolean isValidFile(BufferedInputStream ins) throws IOException
diff --git a/debian/patches/series b/debian/patches/series
index d2aec8c..9e6f070 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -4,3 +4,4 @@ test-classpath.patch
 CRAMReferenceSequenceFile.patch
 java-8-sort.patch
 picard-api-change.patch
+htsjdk-api-change.patch

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/artemis.git

More information about the debian-med-commit mailing list