File Changes for wong

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

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