Commits for vsmalladi

v244_base to v245_preview (2010-12-07 to 2010-12-14) v245

• Updated the Composite Long and Short Labels to correspond with track label standards.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra - lines changed 2, context: html, text, full: html, text
• Updated default view of Peaks from Dense to Peak.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra - lines changed 1, context: html, text, full: html, text
• Updated the subTrack Long Labels to match Track label standards.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra - lines changed 48, context: html, text, full: html, text
• Updated Short label abbreviations: Changed Raw Signal Shortlabels to not include anything except Cell.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra - lines changed 12, context: html, text, full: html, text
• Update Composite Long to follow track label standard.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra - lines changed 8, context: html, text, full: html, text
• Updated comments
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra - lines changed 6, context: html, text, full: html, text
• Updated Long Labels to follow track label conventions
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra - lines changed 338, context: html, text, full: html, text
• Updated Short Labels with appropirate abbreviations.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra - lines changed 255, context: html, text, full: html, text
• Updated Composite long label to follow track label conventions.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra - lines changed 1, context: html, text, full: html, text
• Updated long labels to follow track label guide.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra - lines changed 142, context: html, text, full: html, text
• Updated short labels to follow track label guide and provided description in the Track Configuration Page.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.html - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra - lines changed 131, context: html, text, full: html, text
• Updated comments in trackDb about configuration.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra - lines changed 14, context: html, text, full: html, text
• Updated comments in trackDb and fixed errors in description page.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra - lines changed 2, context: html, text, full: html, text
• Updated comments in trackDb pages.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra - lines changed 15, context: html, text, full: html, text
• Removed indents and replaced with bullet points.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.html - lines changed 5, context: html, text, full: html, text
• Updated the validationSettings for OpenChromatin Labs to include nMatch,isSort options.
  • src/hg/encode/DAFs/2.0/dukeDnaseSeq.daf - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/uncFaireSeq.daf - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/utAustinChipSeq.daf - lines changed 1, context: html, text, full: html, text
• Removed validateFastq option and use default settings for fastq validation.
  • src/hg/encode/DAFs/2.0/haibChipSeq.daf - lines changed 2, context: html, text, full: html, text
• Added 7 submissions to track and display.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra - lines changed 805, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra - lines changed 191, context: html, text, full: html, text
• Added 205 Uniform signal tracks generated by Anshul and AWG. replaced about 36 existing signals with updated signals and meta-data.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 3742, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 2192, context: html, text, full: html, text
• Fixed li tag problem to be enclosed by ul tag.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.html - lines changed 2, context: html, text, full: html, text
• Removed errant </h2> tag
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.html - lines changed 1, context: html, text, full: html, text
• Fixed problems that robot detected in html format.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.html - lines changed 9, context: html, text, full: html, text
• Replaced methyl27 include with wgEncodeHaibMethylArray as files have changed.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
• Updated the DAF for the PSU Histone track, which was previously inconsistent with the TFBS track.
  • src/hg/encode/DAFs/2.0/psuMm9Histone.daf - lines changed 20, context: html, text, full: html, text
• Updated version from 1.5 to 1.6
  • src/hg/encode/DAFs/2.0/psuMm9Histone.daf - lines changed 1, context: html, text, full: html, text
• Added Mel CTCF experiment to track.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra - lines changed 151, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra - lines changed 22, context: html, text, full: html, text
• Made new composite for PSU Histone data, added meta-data file for new composite also. 5 total submission were loaded are displayed.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra - lines changed 601, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra - lines changed 155, context: html, text, full: html, text
• Updated track labels, short and long.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra - lines changed 2, context: html, text, full: html, text
• Fixed typo of /ul with /li which is correct.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.html - lines changed 1, context: html, text, full: html, text
• Updated the default Signals and view's limits of Signals. Turned default track visibility as full.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra - lines changed 17, context: html, text, full: html, text
• Added 13 new submissions to trackDb and metaDb.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 3673, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra - lines changed 678, context: html, text, full: html, text
• Added submission 1968 to track.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra - lines changed 90, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra - lines changed 26, context: html, text, full: html, text
• Added release tags back into track to fix track visibile in supertrack configuration page on RR.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.ra - lines changed 155, context: html, text, full: html, text
• Removed reference fleCatV17e, according to Redmine issue 1609.
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• Updated display conventions for track. Need to update default tracks that are shown.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 53, context: html, text, full: html, text
• Commented out duplicte cell lines obtained by multiple lines. Choose the Yale Cell combination that had the largest file size when adding two replicates. Also updated the track matrix to be between Cell line and Treatment.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra - lines changed 88, context: html, text, full: html, text
• Added short label abbreviations for Hot Spots and Raw Signal as Hspt and Raw respectivley. Updated forced ordering within browser of K562 and HepG2 to be first and second respectivley regardless of alphabeticall reordering within browser.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra - lines changed 35, context: html, text, full: html, text
• Added release 1 directory of the Mouse SYDH first mouse track.
  • src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhTfbs.release1.notes - lines changed 138, context: html, text, full: html, text
• Revoked 13 experiments see Redmine issue #55
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra - lines changed 644, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra - lines changed 140, context: html, text, full: html, text
• Added new variable treatment to UW tracks.
  • src/hg/encode/DAFs/2.0/uwDnaseDgf.daf - lines changed 4, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/uwDnaseSeq.daf - lines changed 4, context: html, text, full: html, text
• Removed tables for 5 lab specific experiments, total of 9 tables removed.
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibMethylRrbs.release1.notes - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra - lines changed 10, context: html, text, full: html, text
• Updated ordering of Tier 1 cells to be alphabetical. Ordered Tier 1 and 2 cells to force them to be ahead of Tier 3 cells which are ordered alphabetically.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra - lines changed 13, context: html, text, full: html, text
• Removed Lab specific information from labels and track description.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra - lines changed 248, context: html, text, full: html, text
• Added Short Label for Hot Spots: Hspt. Also updated default tracks on to be Replicate 1 only for All Tier 1 cell and HepG2, 1 tier 2.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra - lines changed 130, context: html, text, full: html, text
• Updated Track Long label and reverted track short labels back to normal convention, reversing truncation rules used earlier. Updated Short labels for Views to be consistent with DNaseI and DGF tracks.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra - lines changed 378, context: html, text, full: html, text
• Updated Long Labels to follow track labeling conventions.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra - lines changed 423, context: html, text, full: html, text
• Fixed long label to include by, typo last time.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra - lines changed 2, context: html, text, full: html, text
• Added release notes to fufill Redmine issue #1465
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.html - lines changed 17, context: html, text, full: html, text
• Inserted reference to wrong number of Bad Bams, had 5 instead of 4.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.html - lines changed 1, context: html, text, full: html, text
• Added missing ( around Peaks.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.html - lines changed 1, context: html, text, full: html, text
• Added missing input for HCFaa and HBMEC.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.ra - lines changed 20, context: html, text, full: html, text
• Updated track long label according to track label conventions. Fixed shortlabels to not use abbreviation of cells and factors. Update shortlabel view to match other UW track.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.ra - lines changed 226, context: html, text, full: html, text
• Updated View long labels to match track labeling conventions.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.ra - lines changed 243, context: html, text, full: html, text