File Changes for vsmalladi

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

• src/hg/encode/DAFs/2.0/licrMm9Histone.daf
  • lines changed 2, context: html, text, full: html, text
    Added nMatch and commented out revisions line
  • lines changed 4, 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/licrMm9Tfbs.daf
  • lines changed 2, context: html, text, full: html, text
    Added nMatch and commented out revisions line
  • lines changed 4, 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/psuMm95c.daf
  • 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/psuMm9DnaseSeq.daf
  • lines changed 2, 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/psuMm9Histone.daf
  • lines changed 2, 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/psuMm9Tfbs.daf
  • lines changed 2, context: html, text, full: html, text
    Updated Hardison Grant labs bam validation (for DNA) and commented out Revision History line/
• src/hg/encode/encodeValidate/config/cv.ra
  • lines changed 2, context: html, text, full: html, text
    Fixed two typos in terms for mouse cell lines (3143 should be 3134 and Cerebrumm should be Cerebrum).
  • lines changed 5, context: html, text, full: html, text
    Added age E0 to the age for embryonic stem cell age
  • lines changed 183, context: html, text, full: html, text
    Updated mouse registered Cell lines registered by UW lab
• src/hg/encode/encodeValidate/test/expected/chipseq/README.txt
  • lines changed 7, 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/load.ra
  • lines changed 16, 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/mdb.txt
  • lines changed 4, 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/trackDb.ra
  • lines changed 24, 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/input/chipseq/StanfordChip-Mouse.DAF
  • lines changed 45, 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/input/chipseq/StanfordChip-Test-Jun08.DDF
  • lines changed 5, 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/input/chipseq/StanfordChip-Test-Mouse.DDF
  • lines changed 5, 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/input/chipseq/StanfordChip.DAF
  • lines changed 13, 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/makefile
  • lines changed 1, 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/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 1176, context: html, text, full: html, text
    Updated Track matrix and metadata
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 753, context: html, text, full: html, text
    Added 7 new submissions. Still prelimary display, needs clean up.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 377, context: html, text, full: html, text
    Added 4 new submissions. 2087-2090
  • lines changed 191, context: html, text, full: html, text
    Removed all metadata for 2 submission: 2041,2042 as advised from lab
  • lines changed 3723, 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/wgEncodeUwHistone.ra
  • lines changed 951, context: html, text, full: html, text
    Add 8 new submissions and accompanying metaData for UW Histone Track
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeHaibRrbs.ra
  • lines changed 1, context: html, text, full: html, text
    Updated Methyl Data to be in one composite
  • lines changed 2, context: html, text, full: html, text
    Updated Track matrix and metadata
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeSydhTfbs.ra
  • lines changed 14, context: html, text, full: html, text
    Added Notes section to provide information on track specifications
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl27.ra
  • lines changed 1, context: html, text, full: html, text
    Updated Methyl Data to be in one composite
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Updated Methyl Data to be in one composite
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra
  • lines changed 3, 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/wgEncodeUwDgf.html
  • lines changed 9, context: html, text, full: html, text
    Updated each track description with feedback provided by the UW lab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra
  • lines changed 282, context: html, text, full: html, text
    Added 7 new submissions. Still prelimary display, needs clean up.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.html
  • lines changed 15, context: html, text, full: html, text
    Updated each track description with feedback provided by the UW lab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
  • lines changed 121, context: html, text, full: html, text
    Added 4 new submissions. 2087-2090
  • lines changed 60, context: html, text, full: html, text
    Removed submission 2041 and 2042 as advised by the lab
  • lines changed 1153, 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/wgEncodeUwHistone.html
  • lines changed 13, context: html, text, full: html, text
    Updated each track description with feedback provided by the UW lab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra
  • lines changed 224, context: html, text, full: html, text
    Add 8 new submissions and accompanying metaData for UW Histone Track
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 717, 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.wgEncodeSydhHist.ra
  • lines changed 145, 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.wgEncodeSydhTfbs.ra
  • lines changed 571, 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