Changeset [f8bab821884eb8497727596d8582ebdf906b775f] by Robert Buels

February 1st, 2018 @ 10:53 AM

Merge branch 'master' into show_note_in_additional
https://github.com/GMOD/jbrowse/commit/f8bab821884eb8497727596d8582...

Committed by Robert Buels

  • A src/JBrowse/QueryParamConfigMapper.js
  • A src/JBrowse/Util/dot-object.js
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/.htaccess
  • A tests/js_tests/spec/QueryParamConfigMapper.spec.js
  • A tests/js_tests/spec/SequenceTrack.spec.js
  • A tests/perl_tests/add-bw-track.pl.t
  • A utils/jb_run.js
  • A utils/jb_setup.js
  • A utils/postinstall.js
  • R bin/bam-to-json.pl
  • R bin/wig-to-json.pl
  • R src/wig2png/Makefile.in
  • R src/wig2png/configure
  • R src/wig2png/configure.in
  • R src/wig2png/src/MeanRenderer.cc
  • R src/wig2png/src/WiggleParser.cc
  • R src/wig2png/src/WiggleRangeParser.cc
  • R src/wig2png/src/WiggleTileRenderer.cc
  • R src/wig2png/src/config.h.in
  • R src/wig2png/src/functions.c
  • R src/wig2png/src/macros.h
  • R src/wig2png/src/opts_list.cc
  • R src/wig2png/src/opts_list.h
  • R src/wig2png/src/wig2png.cc
  • R tests/perl_tests/bam-to-json.pl.t
  • R tests/perl_tests/wig-to-json.pl.t
  • R tests/travis.conf
  • M ".gitignore"
  • M ".travis.yml"
  • M Makefile.PL
  • M README.md
  • M bin/add-bw-track.pl
  • M bin/maker2jbrowse
  • M bin/prepare-refseqs.pl
  • M bin/ucsc-to-json.pl
  • M bower.json
  • M build/Makefile
  • M css/genome.css
  • M css/main.css
  • M index.html
  • M package.json
  • M plugins/SVGLollipopTrack/js/SVGFeatures.js
  • M release-notes.txt
  • M sample_data/json/modencode/modencodeMetaData.csv
  • M sample_data/json/modencode/trackList.json
  • M setup.sh
  • M src/JBrowse/Browser.js
  • M src/JBrowse/GenomeView.js
  • M src/JBrowse/JBrowse.profile.js
  • M src/JBrowse/Store/NCList.js
  • M src/JBrowse/Store/NCList_v0.js
  • M src/JBrowse/Store/SeqFeature/BAM.js
  • M src/JBrowse/Store/SeqFeature/NCList.js
  • M src/JBrowse/Store/SeqFeature/UnindexedFasta.js
  • M src/JBrowse/View/DetailsMixin.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/Sequence.js
  • M src/JBrowse/View/Track/_AlignmentsMixin.js
  • M src/JBrowse/View/Track/_FeatureDetailMixin.js
  • M src/JBrowse/init.js
  • M src/JBrowse/main.js
  • M src/perl5/ArrayRepr.pm
  • M src/perl5/Bio/JBrowse/Cmd/BioDBToJson.pm
  • M src/perl5/Bio/JBrowse/Cmd/FormatSequences.pm
  • M src/perl5/Bio/JBrowse/Cmd/RemoveTrack.pm
  • M src/perl5/Bio/JBrowse/FeatureStream.pm
  • M src/perl5/Bio/JBrowse/FeatureStream/BioPerl.pm
  • M src/perl5/Bio/JBrowse/FeatureStream/GFF3_LowLevel.pm
  • M src/perl5/GenomeDB.pm
  • M src/perl5/ImageTrackRenderer.pm
  • M src/perl5/JsonFileStorage.pm
  • M src/perl5/NameHandler.pm
  • M src/perl5/TiledImage.pm
  • M src/perl5/TrackImage.pm
  • M tests/data/hg19_formatted/trackList.json
  • M tests/data/hg19_formatted/tracks/knownGene/chr1/hist-100000-0.jsonz
  • M tests/data/hg19_formatted/tracks/knownGene/chr1/hist-1000000-0.jsonz
  • M tests/data/hg19_formatted/tracks/knownGene/chr1/hist-200000-0.jsonz
  • M tests/data/hg19_formatted/tracks/knownGene/chr1/hist-2000000-0.jsonz
  • M tests/data/hg19_formatted/tracks/knownGene/chr1/hist-500000-0.jsonz
  • M tests/data/hg19_formatted/tracks/knownGene/chr1/lf-1.jsonz
  • M tests/data/hg19_formatted/tracks/knownGene/chr1/lf-10.jsonz
  • M tests/data/hg19_formatted/tracks/knownGene/chr1/lf-11.jsonz
  • M tests/data/hg19_formatted/tracks/knownGene/chr1/lf-2.jsonz
  • M tests/data/hg19_formatted/tracks/knownGene/chr1/lf-3.jsonz
  • M tests/data/hg19_formatted/tracks/knownGene/chr1/lf-4.jsonz
  • M tests/data/hg19_formatted/tracks/knownGene/chr1/lf-5.jsonz
  • M tests/data/hg19_formatted/tracks/knownGene/chr1/lf-6.jsonz
  • M tests/data/hg19_formatted/tracks/knownGene/chr1/lf-7.jsonz
  • M tests/data/hg19_formatted/tracks/knownGene/chr1/lf-8.jsonz
  • M tests/data/hg19_formatted/tracks/knownGene/chr1/lf-9.jsonz
  • M tests/data/hg19_formatted/tracks/knownGene/chr1/trackData.jsonz
  • M tests/data/volvox_formatted_names/.htaccess
  • M tests/data/volvox_formatted_names/names/00e/5.json
  • M tests/data/volvox_formatted_names/names/01f/3.json
  • M tests/data/volvox_formatted_names/names/02e/9.json
  • M tests/data/volvox_formatted_names/names/033/e.json
  • M tests/data/volvox_formatted_names/names/06c/a.json
  • M tests/data/volvox_formatted_names/names/06e/7.json
  • M tests/data/volvox_formatted_names/names/072/7.json
  • M tests/data/volvox_formatted_names/names/07a/b.json
  • M tests/data/volvox_formatted_names/names/082/4.json
  • M tests/data/volvox_formatted_names/names/09f/3.json
  • M tests/data/volvox_formatted_names/names/0f6/e.json
  • M tests/data/volvox_formatted_names/names/0fd/2.json
  • M tests/data/volvox_formatted_names/names/128/a.json
  • M tests/data/volvox_formatted_names/names/129/d.json
  • M tests/data/volvox_formatted_names/names/137/a.json
  • M tests/data/volvox_formatted_names/names/14f/c.json
  • M tests/data/volvox_formatted_names/names/150/3.json
  • M tests/data/volvox_formatted_names/names/15b/0.json
  • M tests/data/volvox_formatted_names/names/192/f.json
  • M tests/data/volvox_formatted_names/names/1ae/d.json
  • M tests/data/volvox_formatted_names/names/1af/d.json
  • M tests/data/volvox_formatted_names/names/1be/0.json
  • M tests/data/volvox_formatted_names/names/1c7/e.json
  • M tests/data/volvox_formatted_names/names/1e9/9.json
  • M tests/data/volvox_formatted_names/names/1ed/8.json
  • M tests/data/volvox_formatted_names/names/220/b.json
  • M tests/data/volvox_formatted_names/names/241/a.json
  • M tests/data/volvox_formatted_names/names/24f/f.json
  • M tests/data/volvox_formatted_names/names/262/f.json
  • M tests/data/volvox_formatted_names/names/265/5.json
  • M tests/data/volvox_formatted_names/names/285/c.json
  • M tests/data/volvox_formatted_names/names/290/d.json
  • M tests/data/volvox_formatted_names/names/2af/d.json
  • M tests/data/volvox_formatted_names/names/2be/0.json
  • M tests/data/volvox_formatted_names/names/304/0.json
  • M tests/data/volvox_formatted_names/names/305/6.json
  • M tests/data/volvox_formatted_names/names/354/6.json
  • M tests/data/volvox_formatted_names/names/35e/6.json
  • M tests/data/volvox_formatted_names/names/36d/e.json
  • M tests/data/volvox_formatted_names/names/376/0.json
  • M tests/data/volvox_formatted_names/names/37b/9.json
  • M tests/data/volvox_formatted_names/names/38b/2.json
  • M tests/data/volvox_formatted_names/names/38d/4.json
  • M tests/data/volvox_formatted_names/names/392/5.json
  • M tests/data/volvox_formatted_names/names/396/5.json
  • M tests/data/volvox_formatted_names/names/3e5/6.json
  • M tests/data/volvox_formatted_names/names/3f4/6.json
  • M tests/data/volvox_formatted_names/names/3f9/a.json
  • M tests/data/volvox_formatted_names/names/430/7.json
  • M tests/data/volvox_formatted_names/names/449/1.json
  • M tests/data/volvox_formatted_names/names/463/7.json
  • M tests/data/volvox_formatted_names/names/480/6.json
  • M tests/data/volvox_formatted_names/names/49a/8.json
  • M tests/data/volvox_formatted_names/names/49a/b.json
  • M tests/data/volvox_formatted_names/names/4f1/7.json
  • M tests/data/volvox_formatted_names/names/4f5/9.json
  • M tests/data/volvox_formatted_names/names/508/8.json
  • M tests/data/volvox_formatted_names/names/510/6.json
  • M tests/data/volvox_formatted_names/names/515/1.json
  • M tests/data/volvox_formatted_names/names/517/9.json
  • M tests/data/volvox_formatted_names/names/519/5.json
  • M tests/data/volvox_formatted_names/names/51a/6.json
  • M tests/data/volvox_formatted_names/names/52f/8.json
  • M tests/data/volvox_formatted_names/names/532/b.json
  • M tests/data/volvox_formatted_names/names/54a/f.json
  • M tests/data/volvox_formatted_names/names/564/c.json
  • M tests/data/volvox_formatted_names/names/575/d.json
  • M tests/data/volvox_formatted_names/names/577/0.json
  • M tests/data/volvox_formatted_names/names/59f/8.json
  • M tests/data/volvox_formatted_names/names/5de/7.json
  • M tests/data/volvox_formatted_names/names/5e1/2.json
  • M tests/data/volvox_formatted_names/names/5fe/e.json
  • M tests/data/volvox_formatted_names/names/634/0.json
  • M tests/data/volvox_formatted_names/names/643/9.json
  • M tests/data/volvox_formatted_names/names/64b/0.json
  • M tests/data/volvox_formatted_names/names/64f/3.json
  • M tests/data/volvox_formatted_names/names/660/8.json
  • M tests/data/volvox_formatted_names/names/668/a.json
  • M tests/data/volvox_formatted_names/names/6b5/2.json
  • M tests/data/volvox_formatted_names/names/6bf/3.json
  • M tests/data/volvox_formatted_names/names/6d2/6.json
  • M tests/data/volvox_formatted_names/names/6eb/9.json
  • M tests/data/volvox_formatted_names/names/6ee/c.json
  • M tests/data/volvox_formatted_names/names/70c/f.json
  • M tests/data/volvox_formatted_names/names/710/9.json
  • M tests/data/volvox_formatted_names/names/731/2.json
  • M tests/data/volvox_formatted_names/names/73a/f.json
  • M tests/data/volvox_formatted_names/names/748/0.json
  • M tests/data/volvox_formatted_names/names/75d/0.json
  • M tests/data/volvox_formatted_names/names/780/5.json
  • M tests/data/volvox_formatted_names/names/78c/4.json
  • M tests/data/volvox_formatted_names/names/79c/3.json
  • M tests/data/volvox_formatted_names/names/79f/7.json
  • M tests/data/volvox_formatted_names/names/7b4/b.json
  • M tests/data/volvox_formatted_names/names/7b6/6.json
  • M tests/data/volvox_formatted_names/names/7bf/e.json
  • M tests/data/volvox_formatted_names/names/7c4/f.json
  • M tests/data/volvox_formatted_names/names/7ce/0.json
  • M tests/data/volvox_formatted_names/names/7e3/3.json
  • M tests/data/volvox_formatted_names/names/7ea/1.json
  • M tests/data/volvox_formatted_names/names/7fa/d.json
  • M tests/data/volvox_formatted_names/names/7fc/3.json
  • M tests/data/volvox_formatted_names/names/815/f.json
  • M tests/data/volvox_formatted_names/names/83a/a.json
  • M tests/data/volvox_formatted_names/names/847/f.json
  • M tests/data/volvox_formatted_names/names/85f/4.json
  • M tests/data/volvox_formatted_names/names/87b/4.json
  • M tests/data/volvox_formatted_names/names/895/9.json
  • M tests/data/volvox_formatted_names/names/8a5/2.json
  • M tests/data/volvox_formatted_names/names/8b4/f.json
  • M tests/data/volvox_formatted_names/names/8ca/f.json
  • M tests/data/volvox_formatted_names/names/8d2/2.json
  • M tests/data/volvox_formatted_names/names/8e1/6.json
  • M tests/data/volvox_formatted_names/names/90b/6.json
  • M tests/data/volvox_formatted_names/names/932/4.json
  • M tests/data/volvox_formatted_names/names/937/b.json
  • M tests/data/volvox_formatted_names/names/945/b.json
  • M tests/data/volvox_formatted_names/names/949/1.json
  • M tests/data/volvox_formatted_names/names/952/e.json
  • M tests/data/volvox_formatted_names/names/9c5/0.json
  • M tests/data/volvox_formatted_names/names/9d8/7.json
  • M tests/data/volvox_formatted_names/names/9dd/b.json
  • M tests/data/volvox_formatted_names/names/9df/1.json
  • M tests/data/volvox_formatted_names/names/9e1/e.json
  • M tests/data/volvox_formatted_names/names/9e3/4.json
  • M tests/data/volvox_formatted_names/names/9fb/b.json
  • M tests/data/volvox_formatted_names/names/a04/4.json
  • M tests/data/volvox_formatted_names/names/a09/8.json
  • M tests/data/volvox_formatted_names/names/a12/d.json
  • M tests/data/volvox_formatted_names/names/a19/3.json
  • M tests/data/volvox_formatted_names/names/a1e/3.json
  • M tests/data/volvox_formatted_names/names/a3f/3.json
  • M tests/data/volvox_formatted_names/names/a63/4.json
  • M tests/data/volvox_formatted_names/names/a71/a.json
  • M tests/data/volvox_formatted_names/names/abe/7.json
  • M tests/data/volvox_formatted_names/names/acc/6.json
  • M tests/data/volvox_formatted_names/names/ad1/d.json
  • M tests/data/volvox_formatted_names/names/ad6/d.json
  • M tests/data/volvox_formatted_names/names/ad7/7.json
  • M tests/data/volvox_formatted_names/names/aec/4.json
  • M tests/data/volvox_formatted_names/names/b01/e.json
  • M tests/data/volvox_formatted_names/names/b12/2.json
  • M tests/data/volvox_formatted_names/names/b16/e.json
  • M tests/data/volvox_formatted_names/names/b39/5.json
  • M tests/data/volvox_formatted_names/names/b67/f.json
  • M tests/data/volvox_formatted_names/names/b7a/8.json
  • M tests/data/volvox_formatted_names/names/ba4/d.json
  • M tests/data/volvox_formatted_names/names/bda/a.json
  • M tests/data/volvox_formatted_names/names/bdd/a.json
  • M tests/data/volvox_formatted_names/names/bf0/1.json
  • M tests/data/volvox_formatted_names/names/c00/f.json
  • M tests/data/volvox_formatted_names/names/c06/8.json
  • M tests/data/volvox_formatted_names/names/c1e/5.json
  • M tests/data/volvox_formatted_names/names/c3b/f.json
  • M tests/data/volvox_formatted_names/names/c46/b.json
  • M tests/data/volvox_formatted_names/names/c4e/6.json
  • M tests/data/volvox_formatted_names/names/c64/f.json
  • M tests/data/volvox_formatted_names/names/c71/1.json
  • M tests/data/volvox_formatted_names/names/ca3/8.json
  • M tests/data/volvox_formatted_names/names/caa/c.json
  • M tests/data/volvox_formatted_names/names/cca/7.json
  • M tests/data/volvox_formatted_names/names/cf0/b.json
  • M tests/data/volvox_formatted_names/names/cf6/6.json
  • M tests/data/volvox_formatted_names/names/d03/a.json
  • M tests/data/volvox_formatted_names/names/d05/0.json
  • M tests/data/volvox_formatted_names/names/d06/2.json
  • M tests/data/volvox_formatted_names/names/d07/b.json
  • M tests/data/volvox_formatted_names/names/d08/4.json
  • M tests/data/volvox_formatted_names/names/d0e/5.json
  • M tests/data/volvox_formatted_names/names/d13/2.json
  • M tests/data/volvox_formatted_names/names/d25/4.json
  • M tests/data/volvox_formatted_names/names/d39/4.json
  • M tests/data/volvox_formatted_names/names/d6f/f.json
  • M tests/data/volvox_formatted_names/names/d75/3.json
  • M tests/data/volvox_formatted_names/names/da8/0.json
  • M tests/data/volvox_formatted_names/names/ddc/3.json
  • M tests/data/volvox_formatted_names/names/de8/3.json
  • M tests/data/volvox_formatted_names/names/df6/f.json
  • M tests/data/volvox_formatted_names/names/e04/f.json
  • M tests/data/volvox_formatted_names/names/e07/3.json
  • M tests/data/volvox_formatted_names/names/e0e/d.json
  • M tests/data/volvox_formatted_names/names/e14/e.json
  • M tests/data/volvox_formatted_names/names/e1a/4.json
  • M tests/data/volvox_formatted_names/names/e1b/2.json
  • M tests/data/volvox_formatted_names/names/e24/2.json
  • M tests/data/volvox_formatted_names/names/e25/3.json
  • M tests/data/volvox_formatted_names/names/e46/2.json
  • M tests/data/volvox_formatted_names/names/e4d/8.json
  • M tests/data/volvox_formatted_names/names/e72/b.json
  • M tests/data/volvox_formatted_names/names/e77/5.json
  • M tests/data/volvox_formatted_names/names/e8b/f.json
  • M tests/data/volvox_formatted_names/names/ea1/6.json
  • M tests/data/volvox_formatted_names/names/ea6/b.json
  • M tests/data/volvox_formatted_names/names/eb8/f.json
  • M tests/data/volvox_formatted_names/names/eba/d.json
  • M tests/data/volvox_formatted_names/names/ebd/3.json
  • M tests/data/volvox_formatted_names/names/ee1/5.json
  • M tests/data/volvox_formatted_names/names/ee7/2.json
  • M tests/data/volvox_formatted_names/names/eed/3.json
  • M tests/data/volvox_formatted_names/names/ef2/4.json
  • M tests/data/volvox_formatted_names/names/f07/3.json
  • M tests/data/volvox_formatted_names/names/f1b/f.json
  • M tests/data/volvox_formatted_names/names/f46/a.json
  • M tests/data/volvox_formatted_names/names/f4d/1.json
  • M tests/data/volvox_formatted_names/names/f5b/d.json
  • M tests/data/volvox_formatted_names/names/f73/7.json
  • M tests/data/volvox_formatted_names/names/f78/7.json
  • M tests/data/volvox_formatted_names/names/f85/3.json
  • M tests/data/volvox_formatted_names/names/f85/6.json
  • M tests/data/volvox_formatted_names/names/fa3/b.json
  • M tests/data/volvox_formatted_names/names/fa9/a.json
  • M tests/data/volvox_formatted_names/names/fb2/e.json
  • M tests/data/volvox_formatted_names/names/fb6/8.json
  • M tests/data/volvox_formatted_names/names/fc9/5.json
  • M tests/data/volvox_formatted_names/names/fcc/d.json
  • M tests/data/volvox_formatted_names/names/fce/a.json
  • M tests/data/volvox_formatted_names/names/ffc/2.json
  • M tests/data/volvox_formatted_names/names/meta.json
  • M tests/data/volvox_formatted_names/trackList.json
  • M tests/data/volvox_formatted_refseqs/trackList.json
  • M tests/js_tests/index.html
  • M tests/perl_tests/flatfile-to-json.pl.t
  • M tests/perl_tests/generate-names.pl.t
  • M tests/perl_tests/prepare-refseqs.pl.t
  • M tests/selenium_tests/jbrowse_selenium/JBrowseTest.py
  • M tests/selenium_tests/jbrowse_selenium/track_selectors.py
  • M tests/selenium_tests/volvox_REST_names_test.py
  • M tests/selenium_tests/volvox_biodb_121_test.py
  • M tests/selenium_tests/volvox_biodb_test.py
  • M tests/selenium_tests/yeast_biodb_test.py
New-ticket Create new ticket

Create your profile

Help contribute to this project by taking a few moments to create your personal profile. Create your profile ยป

AJAX Genome Browser