Commits for kate

v278_preview2 to v278_base (2013-01-15 to 2013-01-22) v278

• Able to remove subtrack types and add narrowPeak at composite level if canPack setting is used to work-around incorrect visibility options problem. #9850 ENCODE Uniform DNaseI HS
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.ra - lines changed 128, context: html, text, full: html, text
• Add ENCODE track types to packable list. They've generally been used in track hierarchies where packability appeared as a side-effect.
  • src/hg/lib/trackDbCustom.c - lines changed 3, context: html, text, full: html, text
• Track description wordsmithing
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRegDnaseClustered.release2.html - lines changed 2, context: html, text, full: html, text
• Add explanation of Tier 2* designation in subtrack list. Response to QA. #9850: ENCODE Uniform DNaseI HS
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.html - lines changed 15, context: html, text, full: html, text
• Fixing merge conflict
  • src/hg/makeDb/trackDb/human/hg19/haibTfbs.txt - lines changed 1755, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/.nfs000000001c22961e000002bd - lines changed 43, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/acc.csh - lines changed 43, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/acc.out - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/new.txt - lines changed 127, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/test.csh - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/tfbsRanges.txt - lines changed 1404, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/viewLimits.txt - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.html - lines changed 20, context: html, text, full: html, text
• Restoring corrections lost in a previous reversion (short label length, signalFilter settings, Huh7.5 tablename
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.ra - lines changed 7, context: html, text, full: html, text
• Fix cell line coloring, in response to QA (Question 7). #9850 ENCODE Uniform DNaseI HS
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.ra - lines changed 5, context: html, text, full: html, text
• Add dccAccessions to metadata for merged experiments. #9850 ENCODE Uniform DNaseI HS
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgDnaseUniform.ra - lines changed 15, context: html, text, full: html, text
• Tweak gray scale shading settings to better distinguish differing signal values which are not well distributed. #9850 ENCODE Uniform DNaseI HS
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.ra - lines changed 3, context: html, text, full: html, text
• Using scoreMax in #9850 ENCODE Uniform DNaseI HS, so adding to narrowPeak list. scoreMin already had this
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 2, context: html, text, full: html, text
• Friendlier formatting of long subgroup.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.ra - lines changed 27, context: html, text, full: html, text
• Removing treatment column from fileUi -- it's not very informative and doesn't sort well. The treatment is viewable in the Additional Details. Subject to veto by AQA... #9850 ENCODE Uniform DNaseI HS
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.ra - lines changed 2, context: html, text, full: html, text
• Filling in missing second accession for UW+Duke Th1 dataset, but need to double-check this with AWG as the cell registration for this is not the same (Adult_CD4+_Th1, Th1)
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgDnaseUniform.ra - lines changed 1, context: html, text, full: html, text
• Updating mdb magic number
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgDnaseUniform.ra - lines changed 1, context: html, text, full: html, text
• Adding step for linking md5sum files properly in downloads. Response to QA. #9850 ENCODE Uniform DNaseI HS
  • src/hg/makeDb/doc/encodeDccHg19/awgUniform.txt - lines changed 2, context: html, text, full: html, text
• Advise on use of UCSC accession listed in metadata and File UI. #9850 ENCODE Uniform DNaseI HS
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.html - lines changed 7, context: html, text, full: html, text
• Allow comma separated list for DCC Accession. Added so that integrative analysis tracks that merge experiments can include the underlying experiments (without a lot of additional development for nested experiments or whatever). Used in #9850 ENCODE Uniform DNaseI HS.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text