Pierre Gruet pushed to branch upstream at Debian Med / igv
Commits: 250f4989 by Pierre Gruet at 2026-09-08T20:55:29+02:00 New upstream version 2.19.8+dfsg - - - - - 259 changed files: - .github/workflows/gradle.yml - .gitignore - README.md - build.gradle - gradle.properties - scripts/igv-launcher.bat - scripts/igv.bat - scripts/igv.command - scripts/igv.sh - scripts/igv_hidpi.sh - scripts/igvtools - scripts/igvtools.bat - scripts/igvtools_gui - scripts/igvtools_gui.bat - scripts/igvtools_gui.command - scripts/igvtools_gui_hidpi - scripts/mac.app/Contents/MacOS/IGV - − scripts/mac.app/Contents/MacOS/IGV.sh - − scripts/mac.app/Contents/MacOS/main.c - scripts/readme.txt - src/main/java/module-info.java - − src/main/java/org/apache/tomcat/util/Ascii.java - − src/main/java/org/apache/tomcat/util/HttpDate.java - src/main/java/org/broad/igv/DirectoryManager.java - src/main/java/org/broad/igv/Globals.java - src/main/java/org/broad/igv/aws/S3LoadDialog.java - src/main/java/org/broad/igv/batch/CommandExecutor.java - src/main/java/org/broad/igv/bedpe/BedPERenderer.java - src/main/java/org/broad/igv/bedpe/InteractionTrack.java - src/main/java/org/broad/igv/bedpe/NestedArcRenderer.java - src/main/java/org/broad/igv/bedpe/PEBlockRenderer.java - src/main/java/org/broad/igv/bedpe/ProportionalArcRenderer.java - src/main/java/org/broad/igv/util/encode/DCCEncodeUtils.java → src/main/java/org/broad/igv/encode/DCCEncodeUtils.java - src/main/java/org/broad/igv/util/encode/EncodeFileRecord.java → src/main/java/org/broad/igv/encode/EncodeFileRecord.java - src/main/java/org/broad/igv/util/encode/EncodeTableModel.java → src/main/java/org/broad/igv/encode/EncodeTableModel.java - src/main/java/org/broad/igv/util/encode/EncodeFileBrowser.java → src/main/java/org/broad/igv/encode/EncodeTrackChooser.java - src/main/java/org/broad/igv/util/encode/UCSCEncodeUtils.java → src/main/java/org/broad/igv/encode/UCSCEncodeUtils.java - src/main/java/org/broad/igv/feature/BasicFeature.java - src/main/java/org/broad/igv/feature/Exon.java - src/main/java/org/broad/igv/feature/FeatureDB.java - src/main/java/org/broad/igv/feature/FeatureUtils.java - src/main/java/org/broad/igv/feature/GFFParser.java - src/main/java/org/broad/igv/feature/genome/ChromAlias.java - src/main/java/org/broad/igv/feature/genome/ChromAliasBB.java - src/main/java/org/broad/igv/feature/genome/ChromAliasDefaults.java - src/main/java/org/broad/igv/feature/genome/ChromAliasFile.java - src/main/java/org/broad/igv/feature/genome/ChromAliasManager.java - src/main/java/org/broad/igv/feature/genome/ChromAliasSource.java - src/main/java/org/broad/igv/feature/genome/GenomeUtils.java → src/main/java/org/broad/igv/feature/genome/ChromSizesUtils.java - + src/main/java/org/broad/igv/feature/genome/DotGenomeUtils.java - src/main/java/org/broad/igv/feature/genome/Genome.java - + src/main/java/org/broad/igv/feature/genome/GenomeDownloadUtils.java - src/main/java/org/broad/igv/feature/genome/GenomeListItem.java - src/main/java/org/broad/igv/feature/genome/GenomeManager.java - − src/main/java/org/broad/igv/feature/genome/GenomeServerException.java - + src/main/java/org/broad/igv/feature/genome/HGVS.java - src/main/java/org/broad/igv/feature/genome/fasta/FastaIndex.java - src/main/java/org/broad/igv/feature/genome/load/ChromsizesLoader.java - src/main/java/org/broad/igv/feature/genome/load/DotGenomeLoader.java - src/main/java/org/broad/igv/feature/genome/load/FastaGenomeLoader.java - src/main/java/org/broad/igv/feature/genome/load/GenbankLoader.java - src/main/java/org/broad/igv/feature/genome/load/GenomeConfig.java - src/main/java/org/broad/igv/feature/genome/load/GenomeLoader.java - − src/main/java/org/broad/igv/feature/genome/load/GenomeObjectLoader.java - src/main/java/org/broad/igv/feature/genome/load/HubGenomeLoader.java - src/main/java/org/broad/igv/feature/genome/load/JsonGenomeLoader.java - src/main/java/org/broad/igv/feature/genome/load/TrackConfig.java - src/main/java/org/broad/igv/feature/tribble/CodecFactory.java - src/main/java/org/broad/igv/feature/tribble/GFFCodec.java - src/main/java/org/broad/igv/htsget/HtsgetReader.java - src/main/java/org/broad/igv/htsget/HtsgetVariantSource.java - src/main/java/org/broad/igv/lists/GeneListManagerUI.java - src/main/java/org/broad/igv/maf/MultipleAlignmentTrack.java - src/main/java/org/broad/igv/oauth/OAuthProvider.java - src/main/java/org/broad/igv/prefs/Constants.java - src/main/java/org/broad/igv/prefs/IGVPreferences.java - src/main/java/org/broad/igv/prefs/PreferencesEditor.java - src/main/java/org/broad/igv/renderer/BarChartRenderer.java - + src/main/java/org/broad/igv/renderer/DynSeqRenderer.java - src/main/java/org/broad/igv/renderer/PointsRenderer.java - src/main/java/org/broad/igv/renderer/XYPlotRenderer.java - src/main/java/org/broad/igv/sam/Alignment.java - src/main/java/org/broad/igv/sam/AlignmentBlock.java - src/main/java/org/broad/igv/sam/AlignmentBlockImpl.java - src/main/java/org/broad/igv/sam/AlignmentRenderer.java - src/main/java/org/broad/igv/sam/AlignmentTrack.java - src/main/java/org/broad/igv/sam/AlignmentTrackMenu.java - src/main/java/org/broad/igv/sam/BaseAlignmentCounts.java - src/main/java/org/broad/igv/sam/CoverageTrack.java - src/main/java/org/broad/igv/sam/DenseAlignmentCounts.java - src/main/java/org/broad/igv/sam/DotAlignedAlignment.java - src/main/java/org/broad/igv/sam/FeatureWrappedAlignment.java - src/main/java/org/broad/igv/sam/LinkedAlignment.java - src/main/java/org/broad/igv/sam/PairedAlignment.java - src/main/java/org/broad/igv/sam/ReadStats.java - src/main/java/org/broad/igv/sam/ReducedMemoryAlignment.java - src/main/java/org/broad/igv/sam/SAMAlignment.java - + src/main/java/org/broad/igv/sam/SbxUtils.java - src/main/java/org/broad/igv/sam/SparseAlignmentCounts.java - src/main/java/org/broad/igv/sam/SpliceJunctionHelper.java - src/main/java/org/broad/igv/sam/SpliceJunctionTrack.java - src/main/java/org/broad/igv/sam/mods/BaseModificationColors.java - src/main/java/org/broad/igv/sam/mods/BaseModificationSet.java - src/main/java/org/broad/igv/sam/reader/SAMReader.java - src/main/java/org/broad/igv/sam/reader/SamReaderPool.java - src/main/java/org/broad/igv/sashimi/SashimiJunctionRenderer.java - src/main/java/org/broad/igv/sashimi/SashimiPlot.java - src/main/java/org/broad/igv/session/IGVSessionReader.java - src/main/java/org/broad/igv/session/RendererFactory.java - src/main/java/org/broad/igv/session/SessionWriter.java - src/main/java/org/broad/igv/tools/IgvToolsGui.java - src/main/java/org/broad/igv/tools/converters/GFFtoBed.java - src/main/java/org/broad/igv/track/AbstractTrack.java - src/main/java/org/broad/igv/track/CombinedDataTrack.java - src/main/java/org/broad/igv/track/DataSourceTrack.java - src/main/java/org/broad/igv/track/DataTrack.java - src/main/java/org/broad/igv/track/FeatureCollectionSource.java - src/main/java/org/broad/igv/track/FileFormatUtils.java - src/main/java/org/broad/igv/track/SelectableFeatureTrack.java - src/main/java/org/broad/igv/track/SequenceTrack.java - src/main/java/org/broad/igv/track/Track.java - src/main/java/org/broad/igv/track/TrackLoader.java - src/main/java/org/broad/igv/track/TrackMenuUtils.java - src/main/java/org/broad/igv/track/TrackProperties.java - src/main/java/org/broad/igv/track/TribbleFeatureSource.java - src/main/java/org/broad/igv/ucsc/Hub.java - src/main/java/org/broad/igv/ucsc/HubTrackSelectionDialog.java - src/main/java/org/broad/igv/ucsc/bb/BBDataSource.java - src/main/java/org/broad/igv/ucsc/bb/BBFile.java - src/main/java/org/broad/igv/ucsc/bb/BBHeader.java - src/main/java/org/broad/igv/ucsc/bb/BBTotalSummary.java - src/main/java/org/broad/igv/ucsc/bb/BBZoomHeader.java - src/main/java/org/broad/igv/ucsc/twobit/TwoBitIndex.java - src/main/java/org/broad/igv/ucsc/twobit/TwoBitSequence.java - + src/main/java/org/broad/igv/ui/DynamicMenuItemsAdjustmentListener.java - src/main/java/org/broad/igv/ui/IGV.java - src/main/java/org/broad/igv/ui/IGVMenuBar.java - src/main/java/org/broad/igv/ui/Main.java - + src/main/java/org/broad/igv/ui/MenuSelectedListener.java - + src/main/java/org/broad/igv/ui/RecentFileSet.java - + src/main/java/org/broad/igv/ui/RecentUrlsSet.java - + src/main/java/org/broad/igv/ui/StackSet.java - src/main/java/org/broad/igv/ui/WaitCursorManager.java - src/main/java/org/broad/igv/ui/action/BrowseEncodeAction.java - src/main/java/org/broad/igv/ui/action/ExportRegionsMenuAction.java - src/main/java/org/broad/igv/ui/action/LoadFilesMenuAction.java - src/main/java/org/broad/igv/ui/action/LoadFromURLMenuAction.java - src/main/java/org/broad/igv/ui/action/OpenSessionMenuAction.java - src/main/java/org/broad/igv/ui/action/SearchCommand.java - src/main/java/org/broad/igv/ui/action/SelectGenomeAnnotationTracksAction.java - src/main/java/org/broad/igv/ui/action/UCSCGenArkAction.java - src/main/java/org/broad/igv/ui/commandbar/ChromosomeComboBox.java - src/main/java/org/broad/igv/ui/commandbar/GenomeComboBox.java - src/main/java/org/broad/igv/ui/commandbar/GenomeListManager.java - − src/main/java/org/broad/igv/ui/commandbar/GenomeSelectionDialog.java - + src/main/java/org/broad/igv/ui/commandbar/HostedGenomeSelectionDialog.java - src/main/java/org/broad/igv/ui/commandbar/IGVCommandBar.java - src/main/java/org/broad/igv/ui/commandbar/RemoveGenomesDialog.java - src/main/java/org/broad/igv/ui/panel/MainPanel.java - src/main/java/org/broad/igv/ui/panel/ReferenceFrame.java - src/main/java/org/broad/igv/ui/panel/TrackNamePanel.java - src/main/java/org/broad/igv/ui/panel/ZoomSliderPanel.java - src/main/java/org/broad/igv/ui/util/AutosaveMenu.java - src/main/java/org/broad/igv/ui/util/FileDialogUtils.java - src/main/java/org/broad/igv/ui/util/HistoryMenu.java - src/main/java/org/broad/igv/ui/util/LoadFromURLDialog.java - src/main/java/org/broad/igv/ui/util/MessageUtils.java - + src/main/java/org/broad/igv/ui/util/RecentUrlsMenu.java - src/main/java/org/broad/igv/ui/util/UIUtilities.java - src/main/java/org/broad/igv/ui/util/download/Downloader.java - src/main/java/org/broad/igv/util/AmazonUtils.java - src/main/java/org/broad/igv/util/FeatureCache.java - src/main/java/org/broad/igv/util/HttpUtils.java - src/main/java/org/broad/igv/util/LongRunningTask.java - src/main/java/org/broad/igv/util/ParsingUtils.java - src/main/java/org/broad/igv/util/ResourceLocator.java - − src/main/java/org/broad/igv/util/S3Presigner.java - src/main/java/org/broad/igv/util/blat/BlatQueryWindow.java - src/main/java/org/broad/igv/util/collections/LRUCache.java - src/main/java/org/broad/igv/util/stream/IGVSeekableStreamFactory.java - src/main/java/org/broad/igv/variant/VariantTrack.java - src/main/java/org/broad/igv/variant/vcf/VCFVariant.java - src/main/java/slider/RangeSliderDemo.java - + src/main/resources/images/checkbox16.png - + src/main/resources/images/checkboxUn16.png - src/main/resources/org/broad/igv/util/encode/encode.hg18.txt → src/main/resources/org/broad/igv/encode/encode.hg18.txt - src/main/resources/org/broad/igv/util/encode/encode.hg19.txt → src/main/resources/org/broad/igv/encode/encode.hg19.txt - src/main/resources/org/broad/igv/util/encode/encode.mm9.txt → src/main/resources/org/broad/igv/encode/encode.mm9.txt - src/main/resources/org/broad/igv/prefs/preferences.tab - src/test/java/org/broad/igv/AbstractHeadlessTest.java - src/test/java/org/broad/igv/feature/genome/ChromAliasBBTest.java - src/test/java/org/broad/igv/feature/genome/ChromAliasDefaultsTest.java - src/test/java/org/broad/igv/feature/genome/ChromAliasFileTest.java - + src/test/java/org/broad/igv/feature/genome/GenomeDownloadUtilsTest.java - src/test/java/org/broad/igv/feature/genome/GenomeManagerTest.java - src/test/java/org/broad/igv/feature/genome/GenomeTest.java - + src/test/java/org/broad/igv/feature/genome/HGVSTest.java - src/test/java/org/broad/igv/feature/genome/fasta/FastaIndexedSequenceTest.java - src/test/java/org/broad/igv/htsget/HtsgetBAMReaderTest.java - src/test/java/org/broad/igv/htsget/HtsgetReaderTest.java - src/test/java/org/broad/igv/htsget/HtsgetVariantSourceTest.java - src/test/java/org/broad/igv/sam/BisulfiteBaseInfoTest.java - src/test/java/org/broad/igv/sam/DenseAlignmentCountsTest.java - src/test/java/org/broad/igv/sam/cram/CRAMReaderTest.java - src/test/java/org/broad/igv/sam/cram/IGVReferenceSourceTest.java - src/test/java/org/broad/igv/tools/IGVToolsCountTest.java - src/test/java/org/broad/igv/tools/converters/GFFtoBedTest.java - src/test/java/org/broad/igv/track/FileFormatUtilsTest.java - src/test/java/org/broad/igv/ucsc/HubTest.java - src/test/java/org/broad/igv/ucsc/bb/BBDataSourceTest.java - src/test/java/org/broad/igv/ucsc/bb/BBFeatureSourceTest.java - + src/test/java/org/broad/igv/ui/RecentFileSetTest.java - + src/test/java/org/broad/igv/ui/RecentUrlsSetTest.java - + src/test/java/org/broad/igv/ui/StackSetTest.java - − src/test/java/org/broad/igv/util/DataInputStreamWrapper.java - + src/test/java/org/broad/igv/util/FeatureCacheTest.java - src/test/java/org/broad/igv/util/IGVHttpClientUtilsTest.java - src/test/java/org/broad/igv/util/TestUtils.java - src/test/java/org/broad/igv/util/stream/IGVSeekableBufferedStreamTest.java - test/batch/color_coverage_993.txt - test/batch/commands.txt - test/batch/datarange.txt - − test/batch/issue_922.txt - test/batch/loadDataURL.txt - test/batch/many_tracks.txt - test/batch/maxPanelHeight.txt - + test/batch/multiLocus.txt - test/batch/multiple_bams.txt - test/batch/overlay.txt - test/batch/path_with_spaces.txt - test/batch/preference_override.txt - test/batch/relative_paths.txt - test/batch/sampleInfo.txt - test/batch/saveSession.txt - + test/batch/singleLocus.txt - test/batch/sort.txt - test/batch/splice_junctions.txt - + test/data/bam/chr_name_cap.bam - + test/data/bam/chr_name_cap.bam.bai - + test/data/bam/chr_name_cap.sam - + test/data/bam/squeeze.sam - + test/data/bedpe/interleaved_chrs.bedpe - − test/data/fasta/out_order.fa.fai - + test/data/genomes/chromAlias_with_namesets.txt - + test/data/genomes/chromAlias_without_namesets.txt - + test/data/genomes/hg38.json - + test/data/genomes/json/hg38_twobit.json - test/data/hubs/groups.txt - + test/data/hubs/gtexCoverage.txt - + test/data/peak/broadPeak.bed - + test/data/peak/gappedPeak.bed - + test/data/peak/narrowPeak.bed - + test/data/sbx/test_q0_18_93.bam - + test/data/sbx/test_q0_18_93.bam.bai - + test/data/sbx/test_q0_18_93.sam - + test/data/sbx/test_q5_22_39.bam - + test/data/sbx/test_q5_22_39.bam.bai - + test/data/sbx/test_q5_22_39.sam - + test/data/wig/bedgraph.bed The diff was not included because it is too large. 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