Changeset [35de1ee100dceedb0e65c3212e4c3582ebea0e82] by jsmirob

April 22nd, 2013 @ 02:08 PM

Committed by jsmirob

  • A bin/add-json.pl
  • A bin/new-plugin.pl
  • A docs/tutorial/data_files/volvox.filtered.vcf.
  • A docs/tutorial/data_files/volvox.filtered.vcf.
  • A docs/tutorial/data_files/volvox.raw.bcf
  • A docs/tutorial/data_files/volvox.test.vcf.gz
  • A docs/tutorial/data_files/volvox.test.vcf.gz.t
  • A docs/tutorial/data_files/volvox.vcf.conf
  • A img/JBrowseLogo_small.png
  • A img/commonIconsDisabled.png
  • A img/spriteArrows.png
  • A src/JBrowse/Component.js
  • A src/JBrowse/Model/BGZip/BGZBlob.js
  • A src/JBrowse/Model/BGZip/VirtualOffset.js
  • A src/JBrowse/Model/CoverageFeature.js
  • A src/JBrowse/Model/TabixIndex.js
  • A src/JBrowse/Store/SeqFeature/Coverage.js
  • A src/JBrowse/Store/SeqFeature/GlobalStatsEstim
  • A src/JBrowse/Store/SeqFeature/REST.js
  • A src/JBrowse/Store/SeqFeature/SNPCoverage.js
  • A src/JBrowse/Store/SeqFeature/VCFTabix.js
  • A src/JBrowse/Store/SeqFeature/VCFTabix/Parser.
  • A src/JBrowse/Store/SeqFeature/_MismatchesMixin
  • A src/JBrowse/Store/TabixIndexedFile.js
  • A src/JBrowse/Util/FastPromise.js
  • A src/JBrowse/View/DetailsMixin.js
  • A src/JBrowse/View/Dialog/SetHighlight.js
  • A src/JBrowse/View/Dialog/WithActionBar.js
  • A src/JBrowse/View/FeatureGlyph.js
  • A src/JBrowse/View/FeatureGlyph/Alignment.js
  • A src/JBrowse/View/FeatureGlyph/Box.js
  • A src/JBrowse/View/FeatureGlyph/_FeatureLabelMi
  • A src/JBrowse/View/FileDialog/TrackList/VCFTabi
  • A src/JBrowse/View/FileDialog/TrackList/_Indexe
  • A src/JBrowse/View/Track/BlockBased/Block.js
  • A src/JBrowse/View/Track/HTMLVariants.js
  • A src/JBrowse/View/Track/VariantDetailMixin.js
  • A src/JBrowse/View/Track/Wiggle/_Scale.js
  • A src/JBrowse/View/Track/_AlignmentsMixin.js
  • A src/jDataView
  • A src/perl5/Bio/JBrowse/JSON.pm
  • A tests/data/rest_store_test/features/ctgA
  • A tests/data/rest_store_test/stats/global
  • A tests/js_tests/spec/RESTStore.spec.js
  • A tests/js_tests/spec/TabixIndex.spec.js
  • A tests/js_tests/spec/TabixIndexedFile.spec.js
  • A tests/perl_tests/add-json.pl.t
  • A tests/perl_tests/json.t
  • R src/JBrowse/View/Track/Canvas.js
  • R src/JBrowse/View/Track/MismatchesMixin.js
  • M .gitmodules
  • M Makefile.PL
  • M README.md
  • M bin/add-track-json.pl
  • M bin/bam-to-json.pl
  • M bin/prepare-refseqs.pl
  • M bin/ucsc-to-json.pl
  • M bin/wig-to-json.pl
  • M build/Makefile
  • M build/init.js
  • M docs/tutorial/conf_files/volvox.json
  • M docs/tutorial/data_files/volvox-sorted.bam.co
  • M docs/tutorial/data_files/volvox-sorted.bam.co
  • M docs/tutorial/data_files/volvox_microarray.bw
  • M icons.css
  • M index.html
  • M jbrowse_conf.json
  • M main.css
  • M menubar.css
  • M release-notes.txt
  • M sample_data/json/modencode/trackList.json
  • M setup.sh
  • M src/JBrowse/Browser.js
  • M src/JBrowse/ConfigAdaptor/JB_json_v1.js
  • M src/JBrowse/GenomeView.js
  • M src/JBrowse/Model/Location.js
  • M src/JBrowse/Model/NestedFrequencyTable.js
  • M src/JBrowse/Model/SimpleFeature.js
  • M src/JBrowse/Plugin.js
  • M src/JBrowse/Store.js
  • M src/JBrowse/Store/DeferredFeaturesMixin.js
  • M src/JBrowse/Store/DeferredStatsMixin.js
  • M src/JBrowse/Store/LRUCache.js
  • M src/JBrowse/Store/Names/Hash.js
  • M src/JBrowse/Store/Names/LazyTrieDojoData.js
  • M src/JBrowse/Store/RemoteBinaryFile.js
  • M src/JBrowse/Store/SeqFeature.js
  • M src/JBrowse/Store/SeqFeature/BAM.js
  • M src/JBrowse/Store/SeqFeature/BAM/File.js
  • M src/JBrowse/Store/SeqFeature/BAM/LazyFeature.
  • M src/JBrowse/Store/SeqFeature/BigWig.js
  • M src/JBrowse/Store/SeqFeature/BigWig/RequestWo
  • M src/JBrowse/Store/SeqFeature/BigWig/Window.js
  • M src/JBrowse/Store/TrackMetaData.js
  • M src/JBrowse/Util.js
  • M src/JBrowse/View/ConfirmDialog.js
  • M src/JBrowse/View/Export/GFF3.js
  • M src/JBrowse/View/FileDialog/ResourceList.js
  • M src/JBrowse/View/FileDialog/TrackList.js
  • M src/JBrowse/View/FileDialog/TrackList/BAMDriv
  • M src/JBrowse/View/FileDialog/TrackList/BigWigD
  • M src/JBrowse/View/FileDialog/TrackList/GFF3Dri
  • M src/JBrowse/View/GranularRectLayout.js
  • M src/JBrowse/View/InfoDialog.js
  • M src/JBrowse/View/LocationChoiceDialog.js
  • M src/JBrowse/View/LocationList.js
  • M src/JBrowse/View/Track/Alignments.js
  • M src/JBrowse/View/Track/Alignments2.js
  • M src/JBrowse/View/Track/BlockBased.js
  • M src/JBrowse/View/Track/CanvasFeatures.js
  • M src/JBrowse/View/Track/ExportMixin.js
  • M src/JBrowse/View/Track/FeatureCoverage.js
  • M src/JBrowse/View/Track/FeatureDetailMixin.js
  • M src/JBrowse/View/Track/FixedImage.js
  • M src/JBrowse/View/Track/GridLines.js
  • M src/JBrowse/View/Track/HTMLFeatures.js
  • M src/JBrowse/View/Track/LocationScale.js
  • M src/JBrowse/View/Track/SNPCoverage.js
  • M src/JBrowse/View/Track/Sequence.js
  • M src/JBrowse/View/Track/Wiggle/Density.js
  • M src/JBrowse/View/Track/Wiggle/XYPlot.js
  • M src/JBrowse/View/Track/WiggleBase.js
  • M src/JBrowse/View/TrackList/Faceted.js
  • M src/JBrowse/View/TrackList/Simple.js
  • M src/jszlib
  • M src/perl5/Bio/JBrowse/Cmd/BioDBToJson.pm
  • M src/perl5/Bio/JBrowse/Cmd/FlatFileToJson.pm
  • M src/perl5/Bio/JBrowse/Cmd/FormatSequences.pm
  • M src/perl5/Bio/JBrowse/Cmd/RemoveTrack.pm
  • M src/perl5/Bio/JBrowse/HashStore.pm
  • M src/perl5/ImageTrackRenderer.pm
  • M tests/data/volvox_formatted_1_2_1/trackInfo.j
  • M tests/data/volvox_formatted_refseqs/trackList
  • M tests/js_tests/index.html
  • M tests/js_tests/spec/AddFiles.spec.js
  • M tests/js_tests/spec/BAM.spec.js
  • M tests/js_tests/spec/BigWig.spec.js
  • M tests/js_tests/spec/FeatureLayout.spec.js
  • M tests/js_tests/spec/GFF3toJbrowseJsonSpec.js
  • M tests/js_tests/spec/Util.spec.js
  • M tests/perl_tests/biodb-to-json.pl.t
  • M tests/perl_tests/wig-to-json.pl.t
  • M tests/selenium_tests/jbrowse_selenium/JBrowse
  • M tests/selenium_tests/jbrowse_selenium/track_s
  • M tests/selenium_tests/modencode_faceted_tracks
  • M tests/selenium_tests/volvox_biodb_test.py
  • M tests/selenium_tests/yeast_biodb_test.py
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