File Changes for cricket

v243_base to v244_preview (2010-11-02 to 2010-11-16) v244

• src/hg/encode/DAFs/2.0/caltechRnaSeq.daf
  • lines changed 51, context: html, text, full: html, text
    Changed DAF to display gtf files and to take different views based on GENCODE version
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 2, context: html, text, full: html, text
    changed fpkm1&2 type to fpkm, changed insDitrib to insDist as it is in the DAFs
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSunyAlbanyGeneSt.release1.notes
  • lines changed 86, context: html, text, full: html, text
    New notes file for SUNY Tiling
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSunyAlbanyTiling.release1.notes
  • lines changed 60, context: html, text, full: html, text
    New notes file for SUNY Tiling
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 87, context: html, text, full: html, text
    I have merged my labels with Tims for typeOfTerm, I still have the SpecialStory variables to check on
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.html
  • lines changed 8, context: html, text, full: html, text
    changing display to explain U and D, issue#1206
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.ra
  • lines changed 140, context: html, text, full: html, text
    changing display to explain U and D, issue#1206
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.new.ra
  • lines changed 721, context: html, text, full: html, text
    removing a copy of wgEncodeRikenCage.ra
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 473, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 77, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 481, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
  • lines changed 391, context: html, text, full: html, text
    added bioRep
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 15, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra
  • lines changed 4, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 81, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
  • lines changed 639, context: html, text, full: html, text
    added the fastqs from hg18
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra
  • lines changed 19, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 108, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
  • lines changed 119, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
  • lines changed 545, context: html, text, full: html, text
    added fastqs from hg18
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 91, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 52, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 43, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
  • lines changed 1426, context: html, text, full: html, text
    added fastqs from hg18
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 38, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
  • lines changed 624, context: html, text, full: html, text
    added fastqs
  • lines changed 810, context: html, text, full: html, text
    added fastqs from hg18
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 199, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 7, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 43, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
  • lines changed 8828, context: html, text, full: html, text
    added fastqs from hg18
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
  • lines changed 113, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 43, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 201, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 343, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 200, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeYaleRnaSeq.ra
  • lines changed 13, context: html, text, full: html, text
    removed the post ENCODE June Freeze tag
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.ra
  • lines changed 34, context: html, text, full: html, text
    turned the default settings to off for Transfrags
  • lines changed 1, context: html, text, full: html, text
    cell to whole cell
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.html
  • lines changed 2, context: html, text, full: html, text
    Bug 1126, fixed typos
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.ra
  • lines changed 3, context: html, text, full: html, text
    standardizing display
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html
  • lines changed 131, context: html, text, full: html, text
    standardizing display
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    changed K652 to K562
  • lines changed 224, context: html, text, full: html, text
    standardizing display
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.html
  • lines changed 2, context: html, text, full: html, text
    changed Gerlad to GERALD and removed artifactually
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    removed the grey shading option for Transfrags Issue#44Item#68
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
  • lines changed 3, context: html, text, full: html, text
    changed visibility settings
  • lines changed 80, context: html, text, full: html, text
    changed long labels
  • lines changed 1, context: html, text, full: html, text
    changed K652 to K562
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.html
  • lines changed 5, context: html, text, full: html, text
    changed spelling errors and added a sam tools reference
  • lines changed 2, context: html, text, full: html, text
    added information about the custom tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    changed K652 to K562
  • lines changed 13, context: html, text, full: html, text
    cell to whole cell
  • lines changed 1, context: html, text, full: html, text
    changed bam setting to color by strand
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.html
  • lines changed 19, context: html, text, full: html, text
    added 2 new tracks, changed long labels to new model
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.ra
  • lines changed 240, context: html, text, full: html, text
    added 2 new tracks, changed long labels to new model
  • lines changed 1, context: html, text, full: html, text
    changed K652 to K562
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 23, context: html, text, full: html, text
    chnaged long labels to new convention
  • lines changed 2, context: html, text, full: html, text
    changed long labels, added Tier 1 comment
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.ra
  • lines changed 10, context: html, text, full: html, text
    changed long labels, added Tier 1 comment
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.ra
  • lines changed 1, context: html, text, full: html, text
    changed K652 to K562
• src/hg/makeDb/trackDb/human/hg19/wgEncodeYaleRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    changed K652 to K562
• src/hg/utils/automation/Encode.pm
  • lines changed 2, context: html, text, full: html, text
    change freeze date