Commits for kate

v295_preview2 to v295_base (2014-01-27 to 2014-02-03) v295

• Request to split Publications link on ENCODE portal into two (Community vs. Consortium), from John Stam, with Mike P. concurrence (prompted by input from Science editor
  • src/hg/htdocs/ENCODE/index.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/ENCODE/pubsOther.html - lines changed 3, context: html, text, full: html, text
• Brief additions by Mike Pazin.
  • src/hg/htdocs/ENCODE/pubsOther.html - lines changed 8, context: html, text, full: html, text
• Truncate tests to 1000 lines
  • src/utils/bedScore/tests/expected/asinhTest.narrowPeak - lines changed 1000, context: html, text, full: html, text
  • src/utils/bedScore/tests/expected/broadGm12878Ctcf.jan2011.asinh.narrowPeak - lines changed 40006, context: html, text, full: html, text
  • src/utils/bedScore/tests/expected/encodeRegTest.bed - lines changed 44159, context: html, text, full: html, text
  • src/utils/bedScore/tests/expected/encodeStd2Test.bed - lines changed 44159, context: html, text, full: html, text
  • src/utils/bedScore/tests/expected/encodeTfbsTest.bed - lines changed 31461, context: html, text, full: html, text
  • src/utils/bedScore/tests/expected/regTest.narrowPeak - lines changed 1000, context: html, text, full: html, text
  • src/utils/bedScore/tests/expected/std2Test.narrowPeak - lines changed 1000, context: html, text, full: html, text
  • src/utils/bedScore/tests/input/asinhTest.narrowPeak - lines changed 1000, context: html, text, full: html, text
  • src/utils/bedScore/tests/input/broadGm12878Ctcf.jan2011.asinh.narrowPeak - lines changed 40006, context: html, text, full: html, text
  • src/utils/bedScore/tests/input/encodeTfbsTest.bed - lines changed 30515, context: html, text, full: html, text
  • src/utils/bedScore/tests/input/hsmmCtcfJan2011.narrowPeak - lines changed 43159, context: html, text, full: html, text
  • src/utils/bedScore/tests/makefile - lines changed 11, context: html, text, full: html, text
• Fix error check -- allow motif display without DNA sequence (as in dm2 flyReg track)
  • src/hg/hgc/regMotif.c - lines changed 1, context: html, text, full: html, text
• Add some flexibility to Motif section display. refs #9092
  • src/hg/hgc/hgc.h - lines changed 4, context: html, text, full: html, text
  • src/hg/hgc/peakClusters.c - lines changed 3, context: html, text, full: html, text
• Add some flexibility to Motif section display. refs #9092
  • src/hg/hgc/regMotif.c - lines changed 24, context: html, text, full: html, text
• Rearrange sections on factorSource details page and make another sectdion collapsible (motifs section better placed). refs #9092
  • src/hg/hgc/peakClusters.c - lines changed 13, context: html, text, full: html, text
• 1. Bug fix: need section on details page for peak clusters lacking motif. 2. Some code simplification. refs #9092
  • src/hg/hgc/peakClusters.c - lines changed 20, context: html, text, full: html, text
  • src/hg/inc/web.h - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/web.c - lines changed 17, context: html, text, full: html, text
• Remove cell abbreviation table from configuration page. Not needed there and it's quite long
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 10, context: html, text, full: html, text
• Add table of Factorbook aliases for TF genes, so outside link works. Suppress link if there's no page. refs #9092
  • src/hg/hgc/hgc.c - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
• Add multi-select filter for factors to factorSource config page
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 8, context: html, text, full: html, text
  • src/hg/hgTracks/factorSource.c - lines changed 43, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 138, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
• Ignore TF filter on clean cart. refs #9092
  • src/hg/hgTracks/factorSource.c - lines changed 2, context: html, text, full: html, text
• Add UI checkbox to suppress display of cell abbreviations.
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 33, context: html, text, full: html, text
  • src/hg/hgTracks/factorSource.c - lines changed 11, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClusteredV3.html - lines changed 1, context: html, text, full: html, text
• Bump up window size to display motifs
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 2, context: html, text, full: html, text
• Clean up Tfbs Clusters tables
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 2, context: html, text, full: html, text
• Cleanup
  • src/hg/makeDb/doc/encodeRegHg19.txt - lines changed 6, context: html, text, full: html, text
• Remove debug
  • src/hg/hgTracks/factorSource.c - lines changed 1, context: html, text, full: html, text