Commits for vsmalladi
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v263_base to v264_preview (2012-02-14 to 2012-02-21) v264
- Replaced the Freeze date from 'post ENCODE Jan 2011 Freeze' to 'ENCODE Mar 2012 Freeze'. Redmine #4577, #6581.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwRepliSeq.ra - lines changed 353, context: html, text, full: html, text
- Fixed issues found in Redmine #4577
20. Updated pixcel heigh to default to 64 to make viewing data more reasonable
21. Removed sex for BGO2ES cell line as it is stated in the cv.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwRepliSeq.ra - lines changed 23, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra - lines changed 1, context: html, text, full: html, text
- Removed MS-DOS CRLF line terminators.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.html - lines changed 2, context: html, text, full: html, text
- Added treatment as a variable. Redmine #3631.
- src/hg/encode/DAFs/3.0/mm9/wgEncodeUwDgf.daf - lines changed 4, context: html, text, full: html, text
- Added treatment to list of variables. Redmine #4468.
- src/hg/encode/DAFs/3.0/mm9/wgEncodeUwDnase.daf - lines changed 4, context: html, text, full: html, text
- Removed Strain as an expVar since it is not being varried on. Redmine #5986.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 2, context: html, text, full: html, text
- Addeded expIds and accessions for track. Redmine #5986.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 477, context: html, text, full: html, text
- Loaded updated versions of the bam files that were colliding. Updated objStatus on V1 of data. Redmine #5393, note #2. #4931.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra - lines changed 57, context: html, text, full: html, text
- Loaded updated versions of the bam files that were colliding. Updated objStatus on V1 of data. Redmine #5394, note #2. #4931.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra - lines changed 141, context: html, text, full: html, text
- Set default tissues on to be Genital FatPat, Heart, Kidney, Ovary, Spleen and Testis. Redmine #5986.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.ra - lines changed 31, context: html, text, full: html, text
- Fixed dimensions to have cellType on X-axis. Removed age from sortOrder and fileSortOrder. Correct replicate label in fileSortOrder to be just Replicate since we only have UCSC Replicate in metaDb and not UCSC Replicate. Redmine ##5986.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.ra - lines changed 3, context: html, text, full: html, text
- Changed hard link to supplementary from hgdownload to hgdownload-test and from hg19 to mm9. Redmine #5986.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.html - lines changed 1, context: html, text, full: html, text
- Replaced experiment wgEncodeEM001962 with new version using a Std control. Redmine #5397.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 7, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.new.ra - lines changed 14, context: html, text, full: html, text
- Updated long and short labels to follow naming conventions. Used conventions from Human track. Redmine #5986.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.ra - lines changed 243, context: html, text, full: html, text
- Updated track description. Redmine #225.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.html - lines changed 103, context: html, text, full: html, text
- Added some information and removed 2 sentences from the 5C description section. Redmine #2606.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeChromSuper.html - lines changed 3, context: html, text, full: html, text
- Updated long labels and removed extra visibility setting. Redmine #225.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.ra - lines changed 5, context: html, text, full: html, text
- Added md5sum's, expId's and DCCaccession numbers. Redmine #225.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUmassDekker5C.ra - lines changed 139, context: html, text, full: html, text
- Added release1 notes for track. Redmine #225.
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUmassDekker5C.release1.notes - lines changed 115, context: html, text, full: html, text
- Added information about new field platform that is needed for microarray platforms. Redmine #6626.
- src/hg/encode/encodeValidate/config/fields.ra - lines changed 6, context: html, text, full: html, text
- Moved over approved changes from beta/cv.ra to public/cv.ra. Redmine #6966.
- src/hg/makeDb/trackDb/cv/public/cv.ra - lines changed 709, context: html, text, full: html, text
- Fixes track description errors found in Redmine #225
1) Made new sentence after phrase and added comma "however users..."
2) Removed comma in phrase ", by using the built in"
3) Changed "built in" -> "built-in"
4) Removed comma in phrase "strength, with"
5) Changed sentence "Sequencing files are provided in fastQ format" -> "Sequencing files provided in fastQ format"
6) Removed acrynym in 2nd pharagraph and added in first of Methods "transcription start site (TSS)"
7) Changed "transcription start (TSS)" -> "TSS" in 2nd pharagraph of methods
8) Removed "(Tm)"
9) Added comma after Currently in phrase "Currently data"
10) Added Oxford comma in phrase " and H1 human embryonic"
11) Placed html tage for special character in 1st reference
12) Changed "using 5C" -> "using the 5C"
13) Changed "These tracks show" -> "This track shows"
14) Changed "Does not function in a linear fashion" -> "Does not function linearly"
15) Changed "To dramatically increase the 3C throughput, the 5C method was developed" -> "The 5C method was developed to dramatically increase 3C throughput"
16) Changed "The major advantage of LMA is that it can be performed at a very high level of multiplexing using" -> "LMA is advantageous due to a much higher level of multiplexing by using"
17) Changed "correspond precisely" -> "precisely correspond"
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.html - lines changed 16, context: html, text, full: html, text
- Changed type doc to spell full document since doc was getting confused with MS doc format. Also changed type pdf back to document that was done in commit: 09a85f5ed26fcf2664db8e887fd1268e7d3627af.
- src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 5, context: html, text, full: html, text
- Updated daf to use new type document instead of doc. Redmine #6626.
- src/hg/encode/DAFs/3.0/hg19/wgEncodeFsuRepliSeq.daf - lines changed 2, context: html, text, full: html, text
- Fixes found during code review. Redmine #6966.
- src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 74, context: html, text, full: html, text
- Fixed labeling for eGFP-JunB and eGFP-JunD.
- src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 2, context: html, text, full: html, text
- Added labels for Mouse tissues that have trucated terms. Also fixed some provisional labels and moved a comment to the end of a stanza.
- src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 20, context: html, text, full: html, text
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