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 <[email protected]> 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 <[email protected]> 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 <[email protected]> +--- 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 <[email protected]> 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 <[email protected]> */ @@ -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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
