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Changeset [d3e607318ddf1e668f5ad4aa5b82e9c0678e7dfd] by Robert Buels

Revision d3e607318ddf1e668f5ad4aa5b82e9c0678e7dfd, committed by Robert Buels · March 7th, 2012 @ 12:24 PM

140 changed files

  • A Makefile.deploy
  • A bin/cpanm
  • A img/closedhand.cur
  • A img/openhand.cur
  • A js/ArrayRepr.js
  • A js/GridTrack.js
  • A js/StaticTrack.js
  • A lib/ArrayRepr.pm
  • A lib/FeatureTrack.pm
  • A lib/GenomeDB.pm
  • A lib/ImageTrack.pm
  • A lib/IntervalStore.pm
  • A lib/JsonFileStorage.pm
  • A sample_data/raw/Dmel.json
  • A sample_data/raw/tomato.json
  • A sample_data/raw/yeast_gbk/NC_001133.gbk
  • A sample_data/raw/yeast_gbk/NC_001133.gbk.gff
  • A sample_data/raw/yeast_genbank.json
  • A t
  • A tests/data/AU9/seq/refSeqs.json
  • A tests/data/AU9/single_au9_gene.gff3
  • A tests/data/base_pairing/XdecoderStructure.gff
  • A tests/data/base_pairing/mahoney.fa
  • A tests/data/base_pairing/mahoney_formatted/seq/mahoney/0.txt
  • A tests/data/base_pairing/mahoney_formatted/seq/refSeqs.json
  • A tests/data/base_pairing/mahoney_formatted/trackList.json
  • A tests/data/hg19/database/knownGene.sql
  • A tests/data/hg19/database/knownGene.txt.gz
  • A tests/data/hg19/database/trackDb.sql
  • A tests/data/hg19/database/trackDb.txt.gz
  • A tests/data/hg19_chromosomes.fkfa
  • A tests/data/hg19_formatted/trackList.json
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/hist-100000-0.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/hist-1000000-0.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/hist-200000-0.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/hist-2000000-0.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/hist-500000-0.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-1.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-10.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-11.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-2.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-3.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-4.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-5.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-6.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-7.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-8.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-9.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/names.json
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/trackData.jsonz
  • A tests/data/tomato_features.json
  • A tests/data/tomato_features_nclist_with_chunksize_10000.json
  • A tests/data/volvox_formatted_refseqs/seq/ctgA/0.txt
  • A tests/data/volvox_formatted_refseqs/seq/ctgA/1.txt
  • A tests/data/volvox_formatted_refseqs/seq/ctgA/2.txt
  • A tests/data/volvox_formatted_refseqs/seq/ctgB/0.txt
  • A tests/data/volvox_formatted_refseqs/seq/refSeqs.json
  • A tests/data/volvox_formatted_refseqs/trackList.json
  • A tests/perl_tests/00.compile.t
  • A tests/perl_tests/bam-to-json.pl.t
  • A tests/perl_tests/bin/fasta_to_fkfa.pl
  • A tests/perl_tests/bin/fkfa_to_fasta.pl
  • A tests/perl_tests/biodb-to-json.pl.t
  • A tests/perl_tests/draw-basepair-track.pl.t
  • A tests/perl_tests/fakefasta.t
  • A tests/perl_tests/flatfile-to-json.pl.t
  • A tests/perl_tests/lazy_nclist.t
  • A tests/perl_tests/lib/FakeFasta.pm
  • A tests/perl_tests/lib/FileSlurping.pm
  • A tests/perl_tests/nclist.t
  • A tests/perl_tests/prepare-refseqs.pl.t
  • A tests/perl_tests/ucsc-to-json.pl.t
  • A tests/perl_tests/wig-to-json.pl.t
  • A wig2png/Makefile.in
  • A wig2png/configure
  • A wig2png/src/config.h.in
  • A wig2png/src/macros.h
  • A wig2png/src/opts_list.cc
  • A wig2png/src/opts_list.h
  • A wig2png/src/wig2png.cc
  • R Makefile.in
  • R closedhand.cur
  • R openhand.cur
  • R js/UITracks.js
  • R lib/AutoHash.pm
  • R rbuels_TODO.txt
  • R src/config.h
  • R test_harness.html
  • R touch.html
  • R configure
  • R src/config.h.in
  • R src/macros.h
  • R src/opts_list.cc
  • R src/opts_list.h
  • R src/wig2png.cc
  • M .gitignore
  • M Makefile.PL
  • M bin/bam-to-json.pl
  • M bin/biodb-to-json.pl
  • M bin/draw-basepair-track.pl
  • M bin/flatfile-to-json.pl
  • M bin/generate-names.pl
  • M bin/prepare-refseqs.pl
  • M bin/ucsc-to-json.pl
  • M bin/wig-to-json.pl
  • M docs/docs.css
  • M docs/featureglyphs.html
  • M docs/tutorial/conf_files/volvox.json
  • M docs/tutorial/data_files/volvox.fa
  • M docs/tutorial/data_files/volvox.gff3
  • M docs/tutorial/index.html
  • M genome.css
  • M index.html
  • M js/Browser.js
  • M js/FeatureTrack.js
  • M js/GenomeView.js
  • M js/ImageTrack.js
  • M js/LazyArray.js
  • M js/LazyPatricia.js
  • M js/NCList.js
  • M js/SequenceTrack.js
  • M js/Track.js
  • M js/Util.js
  • M js/touchJBrowse.js
  • M lib/BioperlFlattener.pm
  • M lib/ExternalSorter.pm
  • M lib/FastaDatabase.pm
  • M lib/ImageTrackRenderer.pm
  • M lib/JsonGenerator.pm
  • M lib/LazyNCList.pm
  • M lib/LazyPatricia.pm
  • M lib/NCLSorter.pm
  • M lib/NCList.pm
  • M lib/NameHandler.pm
  • M lib/TiledImage.pm
  • M release-notes.txt
  • M tests/selenium_tests/volvox_biodb_test.py
  • M tests/selenium_tests/yeast_biodb_test.py
  • M twiki/JBrowsePlugin.pm
  • M twiki/JBrowsePlugin/Makefile.jbrowse