Commits for cline

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

• (1) Set up a stanza for the UNC/BSU lab, replacing the Giddings-m lab. (2) Registered five new antibodies for the Myers lab
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 99, 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
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 2, 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.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 5, 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
  • src/hg/encode/DAFs/2.0/uncBsuProtgeno.daf - lines changed 40, context: html, text, full: html, text
• Added a data type for the proteogenomic peptide hits to the genome
  • src/hg/lib/encode/peptideMapping.as - lines changed 14, context: html, text, full: html, text
  • src/hg/lib/encode/peptideMapping.sql - lines changed 20, 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/inc/peptideMapping.h - lines changed 70, 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.c - lines changed 166, context: html, text, full: html, text
• Minor tweaks: changed the data type to peptideMapping (which should be registered now, I hope)
  • src/hg/encode/DAFs/2.0/uncBsuProtgeno.daf - lines changed 2, context: html, text, full: html, text
• Added two new treatments for the Myers lab
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 10, context: html, text, full: html, text
• Added peptideMapping to the make file
  • src/hg/lib/makefile - lines changed 1, 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
  • src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh - lines changed 11, context: html, text, full: html, text
• Periodic cv update, everything should be stable
  • src/hg/makeDb/trackDb/cv/beta/cv.ra - lines changed 121, context: html, text, full: html, text
• Set up a better mechanism to get the blocks that are syntenic to mm9
  • src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh - lines changed 13, 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/doc/ucscGenes/hg19.ucscGenes13.csh - lines changed 4, 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/uncBsuProt.daf - lines changed 40, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/uncBsuProtgeno.daf - lines changed 40, 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/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Periodic copying of updates from the alpha version of cv.ra
  • src/hg/makeDb/trackDb/cv/beta/cv.ra - lines changed 1, context: html, text, full: html, text
• Added peptideMapping to the list of extended ENCODE types
  • src/hg/utils/automation/Encode.pm - 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/encode/peptideMapping.sql - lines changed 1, context: html, text, full: html, text