File Changes for vsmalladi

v265_base to v266_preview (2012-03-27 to 2012-04-10) v266

• python/style.txt
  • lines changed 2, context: html, text, full: html, text
    Fixed some typo's.
• src/hg/encode/DAFs/3.0/mm9/wgEncodeCshlLongRnaSeq.daf
  • lines changed 25, context: html, text, full: html, text
    Added in changes to the DAF.
• src/hg/encode/DAFs/3.0/mm9/wgEncodeFsuRepliSeq.daf
  • lines changed 44, context: html, text, full: html, text
    First pass of Mouse DAF for FSU Repli-seq. Redmine #6627.
• src/hg/encode/DAFs/3.0/mm9/wgEncodePsuRnaSeq.daf
  • lines changed 14, context: html, text, full: html, text
    Fixed DAF for track. Redmine #107.
  • lines changed 2, context: html, text, full: html, text
    Added other terms in DDF for track. Redmine #107.
• src/hg/encode/DAFs/3.0/mm9/wgEncodeSydhRnaSeq.daf
  • lines changed 17, context: html, text, full: html, text
    Updated DAF for new Signal data.
• src/hg/encode/antibodyWikiParser/antibodyWikiParser.py
  • lines changed 1, context: html, text, full: html, text
    Changed shebang to the correct syntax to be used for python code.
• src/hg/js/utils.js
  • lines changed 1, context: html, text, full: html, text
    Removed tissueSourceType otherTerms.html link as the term is not present on the page. Redmine #7100.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrTfbs.release1.notes
  • lines changed 2, context: html, text, full: html, text
    Fixed issue regarding replicate 1 of an experiment should have been revoked and replicate 2 and 3 should be reclassified as 1 and 2 respectivley. Redmine #5394, Note #63.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 99, context: html, text, full: html, text
    Added a few mouse cell registrations.
  • lines changed 102, context: html, text, full: html, text
    Registration of new cell lines and treatments for Gilbert lab.
  • lines changed 17, context: html, text, full: html, text
    Added MEP cell line for Hardison lab.
  • lines changed 5, context: html, text, full: html, text
    Updated strain for ES-CJ7 to be a specific 129 strain.
  • lines changed 4, context: html, text, full: html, text
    Removed out dataed term displayName.
  • lines changed 16, context: html, text, full: html, text
    Registered HDAC6.
  • lines changed 3, context: html, text, full: html, text
    Fixed spelling of HDAC6 to be consistent with cv.ra.
  • lines changed 5, context: html, text, full: html, text
    Added Ribo-Zero RNA extract type protocol.
  • lines changed 2, context: html, text, full: html, text
    Fixed spelling of organism.
  • lines changed 1, context: html, text, full: html, text
    Fixed error in protocol name.
  • lines changed 1, context: html, text, full: html, text
    Fixed lab designation for MEP cell type.
  • lines changed 5, context: html, text, full: html, text
    Fixed typo's in cv.ra
  • lines changed 18, context: html, text, full: html, text
    Removed comma in Cell's multiple protocols, which is incorrect syntax.
  • lines changed 1, context: html, text, full: html, text
    Commented out T98G protocol that doesn't exist.
  • lines changed 1, context: html, text, full: html, text
    Fixed tag for diffProtD.
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 18, context: html, text, full: html, text
    Removed comma in Cell's multiple protocols, which is incorrect syntax.
  • lines changed 1, context: html, text, full: html, text
    Commented out T98G protocol that doesn't exist.
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 17, context: html, text, full: html, text
    Removed comma in Cell's multiple protocols, which is incorrect syntax.
  • lines changed 1, context: html, text, full: html, text
    Commented out T98G protocol that doesn't exist.
  • lines changed 2, context: html, text, full: html, text
    Fixed error in order of tag and term in stanza.
  • lines changed 38, context: html, text, full: html, text
    Added in approved submissions from beta/cv.ra to public/cv.ra. Redmine #7433.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeFsuRepliSeq.ra
  • lines changed 21, context: html, text, full: html, text
    Added md5sum's for all tracks after the ENCODE Freeze.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 577, context: html, text, full: html, text
    Added 5 new experiments for the track. Redmine #7510.
  • lines changed 28, context: html, text, full: html, text
    Added md5sum's for all tracks after the ENCODE Freeze.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 580, context: html, text, full: html, text
    Added meta-data that was forgotten to be checked in. Redmine #4486.
  • lines changed 68, context: html, text, full: html, text
    Removed HCT-116 control, which was meant for SYDH Histone track.
  • lines changed 334, context: html, text, full: html, text
    Added md5sum's for all tracks after the ENCODE Freeze.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.html
  • lines changed 166, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.ra
  • lines changed 1, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliSeq.html
  • lines changed 6, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
  • lines changed 4, context: html, text, full: html, text
    Updated track default and track description. Redmine #6626.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliSeq.ra
  • lines changed 28, context: html, text, full: html, text
    Updated track default and track description. Redmine #6626.
  • lines changed 1, context: html, text, full: html, text
    Fixed matrix link. Redmine#6626.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.release3.html
  • lines changed 3, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.release3.ra
  • lines changed 118, context: html, text, full: html, text
    Added 5 new experiments for the track. Redmine #7510.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.html
  • lines changed 6, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.ra
  • lines changed 79, context: html, text, full: html, text
    Added 5 experiments to the track. Redmine #4486.
  • lines changed 8, context: html, text, full: html, text
    Removed HCT-116 control as this is for the histone track.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    Displaying the first 24 experiments from FSU for Mouse. Redmine #6627.
  • lines changed 1, context: html, text, full: html, text
    Added 3 submissions for RNA-seq track. Redmine #107.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 7, context: html, text, full: html, text
    Added md5sum's for files.
  • lines changed 15, context: html, text, full: html, text
    Renamed Alignment files, as there was an error in 2 submissions which had an older daf that didn't require replicates for alignment files. Redmine #4156.
  • lines changed 3, context: html, text, full: html, text
    Fixed typo in metadata surrouding spelling of replicate.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 1837, context: html, text, full: html, text
    Added 34 submissions for more processed non-displayed data. Redmine #7089.
  • lines changed 69, context: html, text, full: html, text
    Added md5sum's for all tracks after the ENCODE Freeze.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeFsuRepliSeq.ra
  • lines changed 1105, context: html, text, full: html, text
    Displaying the first 24 experiments from FSU for Mouse. Redmine #6627.
  • lines changed 35, context: html, text, full: html, text
    Fixed error in meta-data regarding reference to age.
  • lines changed 6, context: html, text, full: html, text
    Added trackDescription and metaData variables. Redmine #6627.
  • lines changed 49, context: html, text, full: html, text
    Added md5sum's for all tracks after the ENCODE Freeze.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 136, context: html, text, full: html, text
    Fixed issue regarding replicate 1 of an experiment should have been revoked and replicate 2 and 3 should be reclassified as 1 and 2 respectivley. Redmine #5394, Note #63.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuRnaSeq.ra
  • lines changed 450, context: html, text, full: html, text
    Added 3 submissions for RNA-seq track. Redmine #107.
  • lines changed 19, context: html, text, full: html, text
    Added md5sum's for all tracks after the ENCODE Freeze.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 625, context: html, text, full: html, text
    Added 1 submission for release 2 of track. Redmine #7516.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHist.ra
  • lines changed 43, context: html, text, full: html, text
    Added md5sum's for files.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 67, context: html, text, full: html, text
    Added md5sum's for files.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 57, context: html, text, full: html, text
    Fixed metadata erore with age and strain for A20, 416B, MEL and mg/ER. Redmine #4469,#4468,#3631.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 79, context: html, text, full: html, text
    Fixed metadata erore with age and strain for A20, 416B, MEL and mg/ER. Redmine #4469,#4468,#3631.
  • lines changed 21, context: html, text, full: html, text
    Updated strain for ES-CJ7 to be a specific 129 strain.
  • lines changed 76, context: html, text, full: html, text
    Added md5sum's for all tracks after the ENCODE Freeze.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra
  • lines changed 115, context: html, text, full: html, text
    Fixed metadata erore with age and strain for A20, 416B, MEL and mg/ER. Redmine #4469,#4468,#3631.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 3, context: html, text, full: html, text
    Displaying the first 24 experiments from FSU for Mouse. Redmine #6627.
  • lines changed 4, context: html, text, full: html, text
    Added 3 submissions for RNA-seq track. Redmine #107.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.ra
  • lines changed 4, context: html, text, full: html, text
    Renamed Alignment files, as there was an error in 2 submissions which had an older daf that didn't require replicates for alignment files. Redmine #4156.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.release2.html
  • lines changed 123, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.release2.ra
  • lines changed 1164, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeFsuRepliSeq.html
  • lines changed 149, context: html, text, full: html, text
    Added trackDescription and metaData variables. Redmine #6627.
  • lines changed 6, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeFsuRepliSeq.ra
  • lines changed 238, context: html, text, full: html, text
    Displaying the first 24 experiments from FSU for Mouse. Redmine #6627.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.release2.html
  • lines changed 222, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.release2.ra
  • lines changed 1, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuRnaSeq.ra
  • lines changed 162, context: html, text, full: html, text
    Added 3 submissions for RNA-seq track. Redmine #107.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.release2.html
  • lines changed 263, context: html, text, full: html, text
    Added 1 submission for release 2 of track. Redmine #7516.
  • lines changed 13, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.release2.ra
  • lines changed 517, context: html, text, full: html, text
    Added 1 submission for release 2 of track. Redmine #7516.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.html
  • lines changed 128, context: html, text, full: html, text
    Added track description for track. Redmine #3631.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.ra
  • lines changed 32, context: html, text, full: html, text
    Fixed metadata erore with age and strain for A20, 416B, MEL and mg/ER. Redmine #4469,#4468,#3631.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.ra
  • lines changed 62, context: html, text, full: html, text
    Fixed metadata erore with age and strain for A20, 416B, MEL and mg/ER. Redmine #4469,#4468,#3631.
  • lines changed 7, context: html, text, full: html, text
    Updated strain for ES-CJ7 to be a specific 129 strain.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.ra
  • lines changed 108, context: html, text, full: html, text
    Fixed metadata erore with age and strain for A20, 416B, MEL and mg/ER. Redmine #4469,#4468,#3631.