Commits for cricket

v263_base to v264_preview (2012-02-14 to 2012-02-21) v264

• We do not allow .doc because they are proprietary, I think that this was meant to mean type document (generic), but it was being interpreted and used to submit Word doc. So I am changing it to pdf. We may need to change it back or come up with something for none pdf documents.
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, context: html, text, full: html, text
• This file was replaced a long time ago with .release2
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.html - lines changed 138, context: html, text, full: html, text
• Adding a daf for new file
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeHaibMethylWgbs.daf - lines changed 38, context: html, text, full: html, text
• Adding the terms for the WGBS track
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 19, context: html, text, full: html, text
• Correcting the CpG to CpGSites for clarity
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeHaibMethylWgbs.daf - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 2, context: html, text, full: html, text
• Changing links to be relative
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.html - lines changed 4, context: html, text, full: html, text
• Some html changes for Jacob, cleaning up some metaData to be consistent.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.ra - lines changed 1, context: html, text, full: html, text
• Adding protocols and fixing the trackDb to have new defualts and to have filterComposite
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 2159, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.ra - lines changed 53, context: html, text, full: html, text
• Removing release 3 protocols, adding one more release 1
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 699, context: html, text, full: html, text
• Updating the DAF
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeCshlLongRnaSeq.daf - lines changed 2, context: html, text, full: html, text
• New release notes adding the protocol docs
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlShortRnaSeq.release2.notes - lines changed 304, context: html, text, full: html, text
• Adding a missing md5sum
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 10, context: html, text, full: html, text
• A better notes file
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlShortRnaSeq.release2.notes - lines changed 308, context: html, text, full: html, text
• Getting submission 5558 in and adding the structure for a new view
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUncBsuProt.daf - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.release2.ra - lines changed 47, context: html, text, full: html, text
• Adding and fixing terms for the Proteogenomics group
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 7, context: html, text, full: html, text
• Adding the bigDataUrl for bigBed bam and bigWig
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
• Trying to add bigBeds, but having issues. Checking it in for others to work on
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.release2.ra - lines changed 14, context: html, text, full: html, text
• Changing the tags back to starting with 1 and 2 because a and b did not work as expected
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.ra - lines changed 204, context: html, text, full: html, text
• http://redmine.soe.ucsc.edu/issues/1634#note-111, A bunch of html
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.html - lines changed 14, context: html, text, full: html, text
• Adding references
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.html - lines changed 9, context: html, text, full: html, text
• Adding missing readType and origAssembly
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 101, context: html, text, full: html, text
• Changed the release policy
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.html - lines changed 3, context: html, text, full: html, text
• Adding the V2 files for the bedRnaElements files that had . in the score
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 276, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra - lines changed 205, context: html, text, full: html, text