Commits for wong

v263_preview2 to v263_base (2011-02-07 to 2012-02-14) v263

• quick fix for parsing error, but there are otehr problem with the script, max and I will go over
  • src/hg/encode/antibodyWikiParser/antibodyWikiParser.py - lines changed 3, context: html, text, full: html, text
• one part didn't ignore comments
  • src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease - lines changed 5, context: html, text, full: html, text
• qa fixes for synth html
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html - lines changed 88, context: html, text, full: html, text
• changed calculation method to round at the end
  • python/lib/ucscgenomics/mkChangeNotes.py - lines changed 2, context: html, text, full: html, text
• added mismatch penalty to encourage contiguous segments of alignment more
  • python/lib/ucscgenomics/ucscUtils.py - lines changed 1, context: html, text, full: html, text
• fixed references
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html - lines changed 5, context: html, text, full: html, text
• removed duplicate tags that broke make
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.ra - lines changed 2, context: html, text, full: html, text
• merge fix
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.ra - lines changed 11, context: html, text, full: html, text
• renaming .new to release3
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.html - lines changed 166, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra - lines changed 1568, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release3.html - lines changed 166, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release3.ra - lines changed 1568, context: html, text, full: html, text
• adding trackDb include for release 3 dgf
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
• short and long labels
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release3.ra - lines changed 147, context: html, text, full: html, text
• fixed some straggling labels
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release3.ra - lines changed 4, context: html, text, full: html, text
• homogenized short labels
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.ra - lines changed 16, context: html, text, full: html, text
• fixed a big where spaces in teh antibody name would name it to the validation document's filename
  • src/hg/encode/antibodyWikiParser/antibodyWikiParser.py - lines changed 2, context: html, text, full: html, text
• added in expIds and accessions for UwDgf
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra - lines changed 241, context: html, text, full: html, text
• added in notes for release 3 uw dgf
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwDgf.release3.notes - lines changed 585, context: html, text, full: html, text
• fixed release date
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html - lines changed 1, context: html, text, full: html, text
• changed it to die on spaces in term name
  • src/hg/encode/antibodyWikiParser/antibodyWikiParser.py - lines changed 4, context: html, text, full: html, text
• made error more descriptive
  • src/hg/encode/antibodyWikiParser/antibodyWikiParser.py - lines changed 1, context: html, text, full: html, text
• updated makefile for anitbody parser wiki
  • src/hg/encode/antibodyWikiParser/makefile - lines changed 16, context: html, text, full: html, text
• fixed visibility settings
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release3.ra - lines changed 3, context: html, text, full: html, text
• fixed defaults, and set max display mode to full
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release3.ra - lines changed 9, context: html, text, full: html, text
• set max display mode back to dense
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release3.ra - lines changed 1, context: html, text, full: html, text
• changed html over to release tag
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release3.ra - lines changed 1, context: html, text, full: html, text
• changed handling of attic objects, and also objects that changed states between old and new for tables and gbdbs
  • python/lib/ucscgenomics/mkChangeNotes.py - lines changed 34, context: html, text, full: html, text
• made it 0 or more spaces before labels
  • python/lib/ucscgenomics/qa.py - lines changed 3, context: html, text, full: html, text
• changed it to no filter on wgEncode
  • src/hg/encode/encodeQaCheckHgdownloadFiles/encodeQaCheckHgdownloadFiles - lines changed 9, context: html, text, full: html, text
• added exception for README.txt (it never shows up in the index)
  • src/hg/encode/encodeQaCheckHgdownloadFiles/encodeQaCheckHgdownloadFiles - lines changed 2, context: html, text, full: html, text
• wrong test unmbering
  • src/hg/encode/qaEncodeTracks2/qaEncodeTracks - lines changed 6, context: html, text, full: html, text
• added in last missing tracks
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra - lines changed 246, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra - lines changed 103, context: html, text, full: html, text
• removing accession tags
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release3.ra - lines changed 80, context: html, text, full: html, text
• fixing error messages for bigBed loader to say bigBed
  • src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 6, context: html, text, full: html, text
• removed extraneous letters
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra - lines changed 1, context: html, text, full: html, text
• added origAssembly=hg19 to new objects
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra - lines changed 110, context: html, text, full: html, text
• qa fixes for uwDgf redmine 5406
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release3.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release3.ra - lines changed 12, context: html, text, full: html, text
• fixed a big that had the initDate broken
  • src/hg/encode/encodeQaInit/encodeQaInit - lines changed 1, context: html, text, full: html, text
• fixed defaults
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release3.ra - lines changed 4, context: html, text, full: html, text
• revoked objects and added md5sums
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra - lines changed 16, context: html, text, full: html, text
• missed some revoked, put in now
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra - lines changed 5, context: html, text, full: html, text
• fixed notes for haib rna seq
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibRnaSeq.release1.notes - lines changed 85, context: html, text, full: html, text
• fixed short labels at labs request
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra - lines changed 397, context: html, text, full: html, text
• forgot to fix the too long ones
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra - lines changed 8, context: html, text, full: html, text
• wgEncodeOpenChromSynth.release2.notes
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromSynth.release2.notes - lines changed 31, context: html, text, full: html, text
• updated notes again, gz md5sum bug rears it's ugly head
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromSynth.release2.notes - lines changed 20, context: html, text, full: html, text
• lab preferred changes to the too long ones
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra - lines changed 4, context: html, text, full: html, text
• forgot to removed held back experiment
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromSynth.release2.notes - lines changed 15, context: html, text, full: html, text
• moving openChromDNase to release2 tag
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.new.ra - lines changed 1492, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra - lines changed 1492, context: html, text, full: html, text
• added in a lot of new tracks to open chrom dnase,a dn amde release 2 html
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra - lines changed 1796, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.html - lines changed 310, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra - lines changed 361, context: html, text, full: html, text
• added functionality to recursively walk back include statements for easier management of .hg.conf files
  • src/hg/utils/automation/HgDb.pm - lines changed 38, context: html, text, full: html, text