File Changes for tdreszer

v243_preview2 to v243_base (2010-10-26 to 2010-11-02) v243

• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 4, context: html, text, full: html, text
    Loader should not fail on preexisting files. That is the validator's job.
  • lines changed 4, context: html, text, full: html, text
    Oops, missed one.
• src/hg/encode/encodeValidate/config/cv.ra
  • lines changed 101, context: html, text, full: html, text
    Added 5 new cell lines, on new SOP and 3 new treatments for Crawford
  • lines changed 20, context: html, text, full: html, text
    Minor corrections to Crawfords most recent cells and treatments
  • lines changed 443, context: html, text, full: html, text
    Added typeOfTerm category to allow defining controlled vocabulary and other metadata terms in one place. Putting this in the cv.ra keeps it coordinated with the cv. This will probably be used by hgEncodeVocab to display term definitions. It should be used by Track Search for the white list of searchble terms and '...' metadata to distinguish linkable terms.
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 490, context: html, text, full: html, text
    Added support for getting antibodies by target. Added support for 'label' as the last field. Added support for labs and dataTypes
  • lines changed 13, context: html, text, full: html, text
    Kate wants antibody as first column of table even though sort is by target, then antibidy
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    Reusable blueLines bg image must distinguish reverse complement, and insideX doesn't do that for some strange reason.
• src/hg/hgTracks/searchTracks.c
  • lines changed 85, context: html, text, full: html, text
    Moved mdb/cv terms white list to mdb library code. Now it can be used both by trackSearch and by metadata '...' table which will have links for select terms to hgEncodeVocab.
• src/hg/inc/mdb.h
  • lines changed 3, context: html, text, full: html, text
    Moved mdb/cv terms white list to mdb library code. Now it can be used both by trackSearch and by metadata '...' table which will have links for select terms to hgEncodeVocab.
• src/hg/lib/hui.c
  • lines changed 13, context: html, text, full: html, text
    Links to controlled vocabulary for antibodies will now use target to get set of antibodies
  • lines changed 170, context: html, text, full: html, text
    Fixed problem with bam views. This fix extended to psl and genePred views which would also have had problems. This code also cleans up bam cfg spacing and adds links to selected cv.ra terms found in the '...' metadata table
• src/hg/lib/mdb.c
  • lines changed 91, context: html, text, full: html, text
    Moved mdb/cv terms white list to mdb library code. Now it can be used both by trackSearch and by metadata '...' table which will have links for select terms to hgEncodeVocab.
  • lines changed 2, context: html, text, full: html, text
    Fixed sizing of whiteList array
• src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt
  • lines changed 235, context: html, text, full: html, text
    Wrangling to get round 2 of Broad's hg19 submissions. Peaks are still missing
• src/hg/makeDb/mdbUpdate/mdbPrint.c
  • lines changed 2, context: html, text, full: html, text
    Fixed help typos
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 2042, context: html, text, full: html, text
    40 resubmissions added/changed a lot of metadata
• src/inc/common.h
  • lines changed 12, context: html, text, full: html, text
    Added sorting routines for slPairs when the val is a string. Will be used by cv terms whitelist
• src/lib/common.c
  • lines changed 29, context: html, text, full: html, text
    Added sorting routines for slPairs when the val is a string. Will be used by cv terms whitelist