[med-svn] [artemis] 02/02: Try to update interface to picard/htsjdk
Afif Elghraoui
afif-guest at moszumanska.debian.org
Thu Dec 24 08:27:07 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository artemis.
commit fb4f74b8d46a9e2eb17ecefe9eea1d4e09375a0c
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Thu Dec 24 00:25:11 2015 -0800
Try to update interface to picard/htsjdk
Updates to java dependencies have broken the build. This patch
works towards resolving #808851.
---
debian/control | 2 +-
debian/patches/picard-api-change.patch | 370 +++++++++++++++++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 2 +-
4 files changed, 373 insertions(+), 2 deletions(-)
diff --git a/debian/control b/debian/control
index 655ca75..afd9638 100644
--- a/debian/control
+++ b/debian/control
@@ -14,7 +14,7 @@ Build-Depends:
liblog4j1.2-java,
libpostgresql-jdbc-java,
picard-tools,
- libsam-java,
+ libhtsjdk-java,
libcommons-net-java,
libbatik-java,
jemboss,
diff --git a/debian/patches/picard-api-change.patch b/debian/patches/picard-api-change.patch
new file mode 100644
index 0000000..94b869b
--- /dev/null
+++ b/debian/patches/picard-api-change.patch
@@ -0,0 +1,370 @@
+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
+@@ -30,10 +30,10 @@
+
+ import javax.swing.JOptionPane;
+
+-import net.sf.picard.reference.FastaSequenceIndex;
+-import net.sf.picard.reference.IndexedFastaSequenceFile;
+-import net.sf.picard.reference.ReferenceSequence;
+-import net.sf.picard.reference.ReferenceSequenceFileFactory;
++import htsjdk.samtools.reference.FastaSequenceIndex;
++import htsjdk.samtools.reference.IndexedFastaSequenceFile;
++import htsjdk.samtools.reference.ReferenceSequence;
++import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
+
+ import uk.ac.sanger.artemis.io.Entry;
+ import uk.ac.sanger.artemis.Options;
+@@ -357,4 +357,4 @@
+ e.printStackTrace();
+ }
+ }
+-}
+\ 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
+@@ -23,9 +23,9 @@
+ */
+ package uk.ac.sanger.artemis.components.alignment;
+
+-import net.sf.picard.reference.ReferenceSequence;
+-import net.sf.picard.reference.ReferenceSequenceFile;
+-import net.sf.samtools.SAMSequenceDictionary;
++import htsjdk.samtools.reference.ReferenceSequence;
++import htsjdk.samtools.reference.ReferenceSequenceFile;
++import htsjdk.samtools.SAMSequenceDictionary;
+ 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
+@@ -107,17 +107,17 @@
+
+ import org.apache.log4j.Level;
+
+-import net.sf.picard.reference.ReferenceSequenceFile;
+-import net.sf.picard.sam.BuildBamIndex;
+-import net.sf.samtools.AlignmentBlock;
+-import net.sf.samtools.SAMException;
+-import net.sf.samtools.SAMFileHeader;
+-import net.sf.samtools.SAMFileReader;
+-import net.sf.samtools.SAMReadGroupRecord;
+-import net.sf.samtools.SAMRecord;
+-import net.sf.samtools.SAMSequenceRecord;
+-import net.sf.samtools.SAMFileReader.ValidationStringency;
+-import net.sf.samtools.util.CloseableIterator;
++import htsjdk.samtools.reference.ReferenceSequenceFile;
++import picard.sam.BuildBamIndex;
++import htsjdk.samtools.AlignmentBlock;
++import htsjdk.samtools.SAMException;
++import htsjdk.samtools.SAMFileHeader;
++import htsjdk.samtools.SAMFileReader;
++import htsjdk.samtools.SAMReadGroupRecord;
++import htsjdk.samtools.SAMRecord;
++import htsjdk.samtools.SAMSequenceRecord;
++import htsjdk.samtools.SAMFileReader.ValidationStringency;
++import htsjdk.samtools.util.CloseableIterator;
+
+ import uk.ac.sanger.artemis.Entry;
+ import uk.ac.sanger.artemis.EntryGroup;
+@@ -536,7 +536,7 @@
+
+ try
+ {
+- Class<?> cls = getClass().getClassLoader().loadClass("net.sf.samtools.ReferenceDiscovery");
++ Class<?> cls = getClass().getClassLoader().loadClass("htsjdk.samtools.ReferenceDiscovery");
+ Field f = cls.getDeclaredField("referenceFactory");
+ f.set(null, referenceFactory);
+ }
+@@ -562,7 +562,7 @@
+ }
+
+
+- //net.sf.samtools.ReferenceDiscovery.referenceFactory.put(bamIndexFile, ref);
++ //htsjdk.samtools.ReferenceDiscovery.referenceFactory.put(bamIndexFile, ref);
+ }
+
+ if(bam.startsWith("ftp"))
+@@ -1001,7 +1001,7 @@
+ readsInView.clear();
+ return;
+ }
+- catch(net.sf.samtools.util.RuntimeIOException re)
++ catch(htsjdk.samtools.util.RuntimeIOException re)
+ {
+ JOptionPane.showMessageDialog(this, re.getMessage());
+ }
+--- artemis.orig/uk/ac/sanger/artemis/components/alignment/BamUtils.java
++++ artemis/uk/ac/sanger/artemis/components/alignment/BamUtils.java
+@@ -28,10 +28,10 @@
+ import java.util.List;
+ import java.util.Vector;
+
+-import net.sf.samtools.AlignmentBlock;
+-import net.sf.samtools.SAMFileReader;
+-import net.sf.samtools.SAMRecord;
+-import net.sf.samtools.util.CloseableIterator;
++import htsjdk.samtools.AlignmentBlock;
++import htsjdk.samtools.SAMFileReader;
++import htsjdk.samtools.SAMRecord;
++import htsjdk.samtools.util.CloseableIterator;
+ 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
+@@ -1,6 +1,6 @@
+ package uk.ac.sanger.artemis.components.alignment;
+
+-import net.sf.samtools.SAMRecord;
++import htsjdk.samtools.SAMRecord;
+
+
+ class BamViewRecord
+--- artemis.orig/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
++++ artemis/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
+@@ -51,8 +51,8 @@
+
+ import uk.ac.sanger.artemis.components.Plot;
+
+-import net.sf.samtools.AlignmentBlock;
+-import net.sf.samtools.SAMRecord;
++import htsjdk.samtools.AlignmentBlock;
++import htsjdk.samtools.SAMRecord;
+
+ public class CoveragePanel extends AbstractGraphPanel
+ {
+--- artemis.orig/uk/ac/sanger/artemis/components/alignment/MappedReads.java
++++ artemis/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;
+
+-import net.sf.samtools.SAMFileReader;
++import htsjdk.samtools.SAMFileReader;
+
+ public class MappedReads
+ {
+--- artemis.orig/uk/ac/sanger/artemis/components/alignment/PairedReadComparator.java
++++ artemis/uk/ac/sanger/artemis/components/alignment/PairedReadComparator.java
+@@ -26,7 +26,7 @@
+
+ import java.util.Comparator;
+
+-import net.sf.samtools.SAMRecord;
++import htsjdk.samtools.SAMRecord;
+
+ 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
+@@ -24,7 +24,7 @@
+ import javax.swing.JScrollPane;
+ import javax.swing.SwingUtilities;
+
+-import net.sf.samtools.SAMReadGroupRecord;
++import htsjdk.samtools.SAMReadGroupRecord;
+
+ class ReadGroupsFrame extends JFrame
+ {
+--- artemis.orig/uk/ac/sanger/artemis/components/alignment/RunSamTools.java
++++ artemis/uk/ac/sanger/artemis/components/alignment/RunSamTools.java
+@@ -26,7 +26,7 @@
+ import java.io.*;
+ import java.util.List;
+
+-import net.sf.samtools.SAMRecord;
++import htsjdk.samtools.SAMRecord;
+
+ /**
+ * 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
+@@ -23,7 +23,7 @@
+
+ import java.util.Vector;
+
+-import net.sf.samtools.SAMRecord;
++import htsjdk.samtools.SAMRecord;
+
+ /**
+ * Test the SAMRecord flag.
+--- artemis.orig/uk/ac/sanger/artemis/components/alignment/SAMRecordFlagPredicate.java
++++ artemis/uk/ac/sanger/artemis/components/alignment/SAMRecordFlagPredicate.java
+@@ -21,7 +21,7 @@
+
+ package uk.ac.sanger.artemis.components.alignment;
+
+-import net.sf.samtools.SAMRecord;
++import htsjdk.samtools.SAMRecord;
+
+ /**
+ * Test the SAMRecord flag.
+--- artemis.orig/uk/ac/sanger/artemis/components/alignment/SAMRecordList.java
++++ artemis/uk/ac/sanger/artemis/components/alignment/SAMRecordList.java
+@@ -53,7 +53,7 @@
+ import uk.ac.sanger.artemis.components.alignment.BamViewRecord;
+
+
+-import net.sf.samtools.SAMRecord;
++import htsjdk.samtools.SAMRecord;
+
+ 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
+@@ -21,7 +21,7 @@
+
+ package uk.ac.sanger.artemis.components.alignment;
+
+-import net.sf.samtools.SAMRecord;
++import htsjdk.samtools.SAMRecord;
+
+ /**
+ * 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
+@@ -26,7 +26,7 @@
+
+ import java.util.Comparator;
+
+-import net.sf.samtools.SAMRecord;
++import htsjdk.samtools.SAMRecord;
+ 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
+@@ -21,7 +21,7 @@
+
+ package uk.ac.sanger.artemis.components.alignment;
+
+-import net.sf.samtools.SAMRecord;
++import htsjdk.samtools.SAMRecord;
+
+ /**
+ * 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
+@@ -42,8 +42,8 @@
+ import uk.ac.sanger.artemis.sequence.Bases;
+ import uk.ac.sanger.artemis.util.OutOfRangeException;
+
+-import net.sf.samtools.AlignmentBlock;
+-import net.sf.samtools.SAMRecord;
++import htsjdk.samtools.AlignmentBlock;
++import htsjdk.samtools.SAMRecord;
+
+ public class SnpPanel extends AbstractGraphPanel
+ {
+--- artemis.orig/uk/ac/sanger/artemis/components/variant/BCFReader.java
++++ artemis/uk/ac/sanger/artemis/components/variant/BCFReader.java
+@@ -34,7 +34,7 @@
+
+ import uk.ac.sanger.artemis.util.FTPSeekableStream;
+
+-import net.sf.samtools.util.BlockCompressedInputStream;
++import htsjdk.samtools.util.BlockCompressedInputStream;
+
+ class BCFReader extends AbstractVCFReader
+ {
+--- artemis.orig/uk/ac/sanger/artemis/components/variant/IOUtils.java
++++ artemis/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;
+
+-import net.sf.samtools.util.BlockCompressedInputStream;
++import htsjdk.samtools.util.BlockCompressedInputStream;
+
+ class IOUtils
+ {
+--- artemis.orig/uk/ac/sanger/artemis/components/variant/TabixReader.java
++++ artemis/uk/ac/sanger/artemis/components/variant/TabixReader.java
+@@ -27,8 +27,8 @@
+
+ /* Contact: Heng Li <hengli at broadinstitute.org> */
+
+-import net.sf.samtools.util.BlockCompressedInputStream;
+-import net.sf.samtools.seekablestream.SeekableStream;
++import htsjdk.samtools.util.BlockCompressedInputStream;
++import htsjdk.samtools.seekablestream.SeekableStream;
+
+ 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
+@@ -86,7 +86,7 @@
+ import javax.swing.border.Border;
+ import javax.swing.border.EmptyBorder;
+
+-import net.sf.samtools.util.BlockCompressedInputStream;
++import htsjdk.samtools.util.BlockCompressedInputStream;
+
+ import org.apache.log4j.Level;
+
+--- artemis.orig/uk/ac/sanger/artemis/io/DocumentEntryFactory.java
++++ artemis/uk/ac/sanger/artemis/io/DocumentEntryFactory.java
+@@ -76,7 +76,7 @@
+ throws IOException, EntryInformationException
+ {
+ if(!System.getProperty("java.version").startsWith("1.5.") &&
+- document.getInputStream() instanceof net.sf.samtools.util.BlockCompressedInputStream)
++ document.getInputStream() instanceof htsjdk.samtools.util.BlockCompressedInputStream)
+ {
+ 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
+@@ -38,7 +38,7 @@
+ import java.util.Set;
+ import java.util.Vector;
+
+-import net.sf.samtools.util.BlockCompressedInputStream;
++import htsjdk.samtools.util.BlockCompressedInputStream;
+
+ 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
+@@ -45,7 +45,7 @@
+ import javax.swing.JOptionPane;
+ import javax.swing.JPanel;
+
+-import net.sf.samtools.util.BlockCompressedInputStream;
++import htsjdk.samtools.util.BlockCompressedInputStream;
+
+ /**
+ * 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
+@@ -15,7 +15,7 @@
+ import org.apache.commons.net.ftp.FTPReply;
+ import org.apache.log4j.Logger;
+
+-import net.sf.samtools.seekablestream.SeekableStream;
++import htsjdk.samtools.seekablestream.SeekableStream;
+
+ /**
+ * 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
+@@ -166,11 +166,11 @@
+ {
+ protected static boolean isValidFile(BufferedInputStream ins) throws IOException
+ {
+- return net.sf.samtools.util.BlockCompressedInputStream.isValidFile(ins);
++ return htsjdk.samtools.util.BlockCompressedInputStream.isValidFile(ins);
+ }
+
+ protected static InputStream getBlockCompressedInputStream(BufferedInputStream ins) throws IOException
+ {
+- return new net.sf.samtools.util.BlockCompressedInputStream(ins);
++ return new htsjdk.samtools.util.BlockCompressedInputStream(ins);
+ }
+ }
diff --git a/debian/patches/series b/debian/patches/series
index 1ffda6e..d2aec8c 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,4 @@ jar-rules.patch
test-classpath.patch
CRAMReferenceSequenceFile.patch
java-8-sort.patch
+picard-api-change.patch
diff --git a/debian/rules b/debian/rules
index c98fe04..a6c2fed 100755
--- a/debian/rules
+++ b/debian/rules
@@ -14,7 +14,7 @@ CUPBOARD = biojava \
log4j-1.2 \
postgresql-jdbc3 \
picard \
- sam \
+ htsjdk \
commons-net \
batik-awt-util \
batik-dom \
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