Changeset [a1dc26f7df64dfeaabc834f964c880e4ec86bbd0] by jsmirob
April 23rd, 2013 @ 07:32 AM
merge fix attempt (still broken)
https://github.com/GMOD/jbrowse/commit/a1dc26f7df64dfeaabc834f964c8...
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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