Commits for vsmalladi

v237_preview to v237_base (2010-07-27 to 2010-08-03) v237

• Fixed two typos in terms for mouse cell lines (3143 should be 3134 and Cerebrumm should be Cerebrum).
  • src/hg/encode/encodeValidate/config/cv.ra - lines changed 2, context: html, text, full: html, text
• Updated Methyl Data to be in one composite
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeHaibRrbs.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl27.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra - lines changed 1, context: html, text, full: html, text
• Split up Stan/Yale TFBS data and Histone data into own trackDb's. Update encode trackDb to have only include statements of the encode composites
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 717, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncodeSydhHist.ra - lines changed 145, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncodeSydhTfbs.ra - lines changed 571, context: html, text, full: html, text
• Added 4 new submissions. 2087-2090
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 377, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra - lines changed 121, context: html, text, full: html, text
• Updated the unit test for ChipSeq. Previously was not working. Also added ability to test BAM file validation and mouse with new daf and ddf combo
  • src/hg/encode/encodeValidate/test/expected/chipseq/README.txt - lines changed 7, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/expected/chipseq/load.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/expected/chipseq/mdb.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/expected/chipseq/trackDb.ra - lines changed 24, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/input/chipseq/StanfordChip-Mouse.DAF - lines changed 45, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/input/chipseq/StanfordChip-Test-Jun08.DDF - lines changed 5, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/input/chipseq/StanfordChip-Test-Mouse.DDF - lines changed 5, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/input/chipseq/StanfordChip.DAF - lines changed 13, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/makefile - lines changed 1, context: html, text, full: html, text
• Updated Hardison Grant labs bam validation (for DNA) and commented out Revision History line/
  • src/hg/encode/DAFs/2.0/psuMm95c.daf - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/psuMm9DnaseSeq.daf - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/psuMm9Histone.daf - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/psuMm9Tfbs.daf - lines changed 2, context: html, text, full: html, text
• Added nMatch and commented out revisions line
  • 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
• Updated Dafs to include updated bam validation lines, and replicates required for Peaks and Signals.
  • src/hg/encode/DAFs/2.0/licrMm9Histone.daf - lines changed 4, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/licrMm9Tfbs.daf - lines changed 4, context: html, text, full: html, text
• Updated Track matrix and metadata
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra - lines changed 1176, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeHaibRrbs.ra - lines changed 2, context: html, text, full: html, text
• Updated Short and long lables to be consistent with the TFBS tracks. Moved data from Dnase supertrack to TFBS supertrack
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra - lines changed 3, context: html, text, full: html, text
• Added Notes section to provide information on track specifications
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeSydhTfbs.ra - lines changed 14, context: html, text, full: html, text
• Removed all metadata for 2 submission: 2041,2042 as advised from lab
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 191, context: html, text, full: html, text
• Removed submission 2041 and 2042 as advised by the lab
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra - lines changed 60, context: html, text, full: html, text
• Added age E0 to the age for embryonic stem cell age
  • src/hg/encode/encodeValidate/config/cv.ra - lines changed 5, context: html, text, full: html, text
• Updated mouse registered Cell lines registered by UW lab
  • src/hg/encode/encodeValidate/config/cv.ra - lines changed 183, context: html, text, full: html, text
• Updated each track description with feedback provided by the UW lab
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.html - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.html - lines changed 13, context: html, text, full: html, text
• Added 38 new submissions. Updated short labels to be consistent with previous data.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 3723, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra - lines changed 1153, context: html, text, full: html, text
• Added 7 new submissions. Still prelimary display, needs clean up.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra - lines changed 753, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra - lines changed 282, context: html, text, full: html, text
• Add 8 new submissions and accompanying metaData for UW Histone Track
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra - lines changed 951, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra - lines changed 224, context: html, text, full: html, text