File Changes for vsmalladi

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

• src/hg/encode/DAFs/2.0/dukeDnaseSeq.daf
  • lines changed 1, context: html, text, full: html, text
    Updated the validationSettings for OpenChromatin Labs to include nMatch,isSort options.
• src/hg/encode/DAFs/2.0/haibChipSeq.daf
  • lines changed 2, context: html, text, full: html, text
    Removed validateFastq option and use default settings for fastq validation.
• src/hg/encode/DAFs/2.0/psuMm9Histone.daf
  • lines changed 20, context: html, text, full: html, text
    Updated the DAF for the PSU Histone track, which was previously inconsistent with the TFBS track.
  • lines changed 1, context: html, text, full: html, text
    Updated version from 1.5 to 1.6
• src/hg/encode/DAFs/2.0/uncFaireSeq.daf
  • lines changed 1, context: html, text, full: html, text
    Updated the validationSettings for OpenChromatin Labs to include nMatch,isSort options.
• src/hg/encode/DAFs/2.0/utAustinChipSeq.daf
  • lines changed 1, context: html, text, full: html, text
    Updated the validationSettings for OpenChromatin Labs to include nMatch,isSort options.
• src/hg/encode/DAFs/2.0/uwDnaseDgf.daf
  • lines changed 4, context: html, text, full: html, text
    Added new variable treatment to UW tracks.
• src/hg/encode/DAFs/2.0/uwDnaseSeq.daf
  • lines changed 4, context: html, text, full: html, text
    Added new variable treatment to UW tracks.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibMethylRrbs.release1.notes
  • lines changed 11, context: html, text, full: html, text
    Removed tables for 5 lab specific experiments, total of 9 tables removed.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhTfbs.release1.notes
  • lines changed 138, context: html, text, full: html, text
    Added release 1 directory of the Mouse SYDH first mouse track.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 10, context: html, text, full: html, text
    Removed tables for 5 lab specific experiments, total of 9 tables removed.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
  • lines changed 90, context: html, text, full: html, text
    Added submission 1968 to track.
  • lines changed 644, context: html, text, full: html, text
    Revoked 13 experiments see Redmine issue #55
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 3673, context: html, text, full: html, text
    Added 13 new submissions to trackDb and metaDb.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 805, context: html, text, full: html, text
    Added 7 submissions to track and display.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 3742, 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/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Replaced methyl27 include with wgEncodeHaibMethylArray as files have changed.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.ra
  • lines changed 155, 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/wgEncodeHaibMethylRrbs.html
  • lines changed 22, context: html, text, full: html, text
    Updated short labels to follow track label guide and provided description in the Track Configuration Page.
  • lines changed 2, context: html, text, full: html, text
    Updated comments in trackDb and fixed errors in description page.
  • lines changed 2, context: html, text, full: html, text
    Fixed li tag problem to be enclosed by ul tag.
  • lines changed 1, context: html, text, full: html, text
    Fixed typo of /ul with /li which is correct.
  • lines changed 34, context: html, text, full: html, text
    Removed Lab specific information from labels and track description.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra
  • lines changed 1, context: html, text, full: html, text
    Updated Composite long label to follow track label conventions.
  • lines changed 142, context: html, text, full: html, text
    Updated long labels to follow track label guide.
  • lines changed 131, context: html, text, full: html, text
    Updated short labels to follow track label guide and provided description in the Track Configuration Page.
  • lines changed 2, context: html, text, full: html, text
    Updated comments in trackDb and fixed errors in description page.
  • lines changed 88, 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.
  • lines changed 13, 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.
  • lines changed 248, context: html, text, full: html, text
    Removed Lab specific information from labels and track description.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra
  • lines changed 26, context: html, text, full: html, text
    Added submission 1968 to track.
  • lines changed 140, context: html, text, full: html, text
    Revoked 13 experiments see Redmine issue #55
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 17, context: html, text, full: html, text
    Updated the default Signals and view's limits of Signals. Turned default track visibility as full.
  • lines changed 678, context: html, text, full: html, text
    Added 13 new submissions to trackDb and metaDb.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra
  • lines changed 191, context: html, text, full: html, text
    Added 7 submissions to track and display.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 2192, 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.
  • lines changed 53, 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/wgEncodeUwDgf.html
  • lines changed 1, context: html, text, full: html, text
    Removed errant </h2> tag
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra
  • lines changed 2, context: html, text, full: html, text
    Updated the Composite Long and Short Labels to correspond with track label standards.
  • lines changed 1, context: html, text, full: html, text
    Updated default view of Peaks from Dense to Peak.
  • lines changed 48, context: html, text, full: html, text
    Updated the subTrack Long Labels to match Track label standards.
  • lines changed 12, context: html, text, full: html, text
    Updated Short label abbreviations: Changed Raw Signal Shortlabels to not include anything except Cell.
  • lines changed 14, context: html, text, full: html, text
    Updated comments in trackDb about configuration.
  • lines changed 5, context: html, text, full: html, text
    Updated comments in trackDb pages.
  • lines changed 35, 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/wgEncodeUwDnase.html
  • lines changed 5, context: html, text, full: html, text
    Removed indents and replaced with bullet points.
  • lines changed 9, context: html, text, full: html, text
    Fixed problems that robot detected in html format.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
  • lines changed 8, context: html, text, full: html, text
    Update Composite Long to follow track label standard.
  • lines changed 6, context: html, text, full: html, text
    Updated comments
  • lines changed 338, context: html, text, full: html, text
    Updated Long Labels to follow track label conventions
  • lines changed 255, context: html, text, full: html, text
    Updated Short Labels with appropirate abbreviations.
  • lines changed 15, context: html, text, full: html, text
    Updated comments in trackDb pages.
  • lines changed 130, 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/wgEncodeUwHistone.html
  • lines changed 17, context: html, text, full: html, text
    Added release notes to fufill Redmine issue #1465
  • lines changed 1, context: html, text, full: html, text
    Inserted reference to wrong number of Bad Bams, had 5 instead of 4.
  • lines changed 1, context: html, text, full: html, text
    Added missing ( around Peaks.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra
  • lines changed 378, 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.
  • lines changed 423, context: html, text, full: html, text
    Updated Long Labels to follow track labeling conventions.
  • lines changed 2, context: html, text, full: html, text
    Fixed long label to include by, typo last time.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.ra
  • lines changed 20, context: html, text, full: html, text
    Added missing input for HCFaa and HBMEC.
  • lines changed 226, 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.
  • lines changed 243, context: html, text, full: html, text
    Updated View long labels to match track labeling conventions.
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    Removed reference fleCatV17e, according to Redmine issue 1609.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
  • lines changed 2, 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/wgEncodePsuHistone.ra
  • lines changed 601, 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/wgEncodePsuTfbs.ra
  • lines changed 151, context: html, text, full: html, text
    Added Mel CTCF experiment to track.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 1, 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/wgEncodePsuHistone.ra
  • lines changed 155, 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/wgEncodePsuTfbs.ra
  • lines changed 22, context: html, text, full: html, text
    Added Mel CTCF experiment to track.
  • lines changed 2, context: html, text, full: html, text
    Updated track labels, short and long.