File Changes for cline

v245_preview2 to v245_base (2010-12-21 to 2011-01-04) v245

• src/hg/encode/DAFs/2.0/uncBsuProt.daf
  • lines changed 40, context: html, text, full: html, text
    Added the subcellular localization variable to the unc/bsu proteogenomics daf file. Adding this variable represents expanding the metadata for this track. Shortened the track name so that there might be room for the localizations in the short names
• src/hg/encode/DAFs/2.0/uncBsuProtgeno.daf
  • lines changed 40, context: html, text, full: html, text
    Added the first version of the UNC/BSU proteogenomics DAF, which was recently reviewed by both Cricket and Kate
  • lines changed 2, context: html, text, full: html, text
    Minor tweaks: changed the data type to peptideMapping (which should be registered now, I hope)
  • lines changed 40, context: html, text, full: html, text
    Added the subcellular localization variable to the unc/bsu proteogenomics daf file. Adding this variable represents expanding the metadata for this track. Shortened the track name so that there might be room for the localizations in the short names
• src/hg/inc/peptideMapping.h
  • lines changed 70, context: html, text, full: html, text
    Adding a header file for a new peptide mapping data type, for results of peptides identified in mass spec experiments mapped to the genome
• src/hg/lib/encode/peptideMapping.as
  • lines changed 14, context: html, text, full: html, text
    Added a data type for the proteogenomic peptide hits to the genome
• src/hg/lib/encode/peptideMapping.c
  • lines changed 166, context: html, text, full: html, text
    Adding a c file for a new peptide mapping data type, for results of peptides identified in mass spec experiments mapped to the genome
• src/hg/lib/encode/peptideMapping.sql
  • lines changed 20, context: html, text, full: html, text
    Added a data type for the proteogenomic peptide hits to the genome
  • lines changed 1, context: html, text, full: html, text
    Changed the key for the peptide mapping, since it appears that the combination of chrom, chromStart, and precursorMz is not unique
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Added peptideMapping to the make file
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 11, context: html, text, full: html, text
    Cleaned up some handling of Rfam to remove species-specific hardcoded references. Replaced a sql-level join with a csh-level bedIntersect
  • lines changed 13, context: html, text, full: html, text
    Set up a better mechanism to get the blocks that are syntenic to mm9
  • lines changed 4, context: html, text, full: html, text
    Attempted a more elegant way to select the hg19 blocks that are syntenic to mm9. At this time, I'm not pleased with the results. I generate a bed file in which the bed blocks are delineated consistently with the mm9 subtrack in the consensus track, but this bed file contains items that map to gaps in the mm9 subtrack
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 99, context: html, text, full: html, text
    (1) Set up a stanza for the UNC/BSU lab, replacing the Giddings-m lab. (2) Registered five new antibodies for the Myers lab
  • lines changed 2, context: html, text, full: html, text
    Fixing a bug noticed by Katrina in code review: an erroneous line break in a hyperlink for the new SETDB1 validation document
  • lines changed 5, context: html, text, full: html, text
    Fixed a number of cases where the antibody target name was of the form <target>_(<vendor_id>), such as ELF1_(SC-631). In these cases, the target should just be <target>, such as ELF1 (or perhaps <target>_(<interaction residues>). This came from a bug in a script that erroneously just copied the entire antibody name into the target field.
  • lines changed 10, context: html, text, full: html, text
    Added two new treatments for the Myers lab
  • lines changed 1, context: html, text, full: html, text
    Changed the sex for the WERI-Rb-1 from male to female, by request of Richard Sandstrom
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 121, context: html, text, full: html, text
    Periodic cv update, everything should be stable
  • lines changed 1, context: html, text, full: html, text
    Periodic copying of updates from the alpha version of cv.ra
• src/hg/utils/automation/Encode.pm
  • lines changed 1, context: html, text, full: html, text
    Added peptideMapping to the list of extended ENCODE types