Commits for vsmalladi

v244_preview to v244_preview2 (2010-11-16 to 2010-11-30) v244

• Revoked bigWigs as they were not generated in correctly by Lab
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 4532, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra - lines changed 1921, context: html, text, full: html, text
• Update the default tracks that were one, since all protocols should be turned on by default for the selected cell, antibody combination
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra - lines changed 2, context: html, text, full: html, text
• Corrected Track Description errors
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.html - lines changed 13, context: html, text, full: html, text
• Added 2395, stalled submission in the Release Q
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra - lines changed 229, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRrbs.ra - lines changed 111, context: html, text, full: html, text
• Updated track configuration for RRBS data to include obtained from
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRrbs.ra - lines changed 130, context: html, text, full: html, text
• Removed growth protocol variables that was in protocol variables in meta-data and cv.ra
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra - lines changed 269, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRrbs.ra - lines changed 43, context: html, text, full: html, text
• Fixed some typo of semi-colon(;) instead of colon(:) in the credits section
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.html - lines changed 4, context: html, text, full: html, text
• Updated the default score value to be 10 and greater
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRrbs.ra - lines changed 3, context: html, text, full: html, text
• Fixed lab value in the DAF
  • src/hg/encode/DAFs/2.0/licrMm9Histone.daf - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/licrMm9Tfbs.daf - lines changed 2, context: html, text, full: html, text
• Added First two submissions for Penn State TFBS data set
  • 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/wgEncodePsuTfbs.ra - lines changed 401, 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/wgEncodePsuTfbs.ra - lines changed 88, context: html, text, full: html, text
• Added 13 submission (download only) for LICR (Ren) lab
  • 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/wgEncodeLicrHistone.ra - lines changed 547, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra - lines changed 811, context: html, text, full: html, text
• Accidently misstyped PSU lab data as Histone instead of TFBS
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile - lines changed 1, context: html, text, full: html, text
• Added 4 new submissions for TFBS track
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 529, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.ra - lines changed 81, context: html, text, full: html, text
• Updated default super track configuration from full to dense
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra - lines changed 1, context: html, text, full: html, text
• Updated composite long label with new conventions
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra - lines changed 1, context: html, text, full: html, text
• Removed Release Notes section to be conistent with process of first release of data
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.html - lines changed 5, context: html, text, full: html, text
• Updated the the Configuration and Display convention section for Signals
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.html - lines changed 3, context: html, text, full: html, text
• Removed line for origAssembly which produced an inncorrect message on hgc details page
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra - lines changed 48, context: html, text, full: html, text
• Fixed noInherit line in trackDb
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra - lines changed 1, context: html, text, full: html, text
• Updated track description to include obtainedBy description
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.html - lines changed 8, context: html, text, full: html, text
• Removed Release 1 notes as Release notes are not necessary for the first release of a track.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.html - lines changed 3, context: html, text, full: html, text
• Updated Methyl RRBS file name to the track name of Methyl RRBS from HaibRrbs to HaibMethylRrbs.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra - lines changed 1112, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRrbs.ra - lines changed 1112, context: html, text, full: html, text
• Updated composite long label format to specs of track settings style guide/
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra - lines changed 1, context: html, text, full: html, text
• Added release Notes for Methyl RRBS Track
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibMethylRrbs.release1.notes - lines changed 280, context: html, text, full: html, text
• Updated Contacts links and header labels in track description.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.html - lines changed 18, context: html, text, full: html, text
• Added RawData view to the daf.
  • src/hg/encode/DAFs/2.0/haibChipSeq.daf - lines changed 8, context: html, text, full: html, text
• Updated track descriptions to have Flo Pauli has primary contact for the given data.
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.html - lines changed 3, context: html, text, full: html, text
• added 30 submissions to SYDH TFBS track
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 3969, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 592, context: html, text, full: html, text
• Added 1 submission to SYDH Histone Track
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 133, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.ra - lines changed 18, context: html, text, full: html, text
• Updated maxDisplayWindow to be used with broadPeaks and upgrade UW DGF track conform to max display window
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.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
• Fixed broken email address for Flo in HudsonAlpha track descriptions
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.html - lines changed 1, context: html, text, full: html, text
• Updated Track Long Label according to track conventions
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.ra - lines changed 1, context: html, text, full: html, text
• Updated track configuration matrix to add third dimension for Treatment.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.ra - lines changed 10, context: html, text, full: html, text
• Removed and renamed the track description pages that existed for SYDh Histone
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.html - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.html - lines changed 131, context: html, text, full: html, text
• Updated track description to include that Bowtie aligner was used.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.html - lines changed 1, context: html, text, full: html, text
• Updated track description to include information about hg18 aligner.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.html - lines changed 3, context: html, text, full: html, text
• added 5 new submissions with Raw Signal
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 4371, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra - lines changed 1846, context: html, text, full: html, text
• changed the long labels to the new order
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.ra - lines changed 8, context: html, text, full: html, text