File Changes for cline

v257_preview2 to v257_base (2011-09-13 to 2011-09-19) v257

• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 81, context: html, text, full: html, text
    Added the peptide mapping format
• src/hg/makeDb/doc/proteins/101005.txt
  • lines changed 62, context: html, text, full: html, text
    (1) Removed an inaccurate sentence from the Unc/Bsu Prot track description page. (2) In the 101005.txt protein database script, added a shell variable to represent the base of the kent source tree. (3) In pbCalDistGlobal, there was an errAbort condition indicating that the number of proteins exceeded the max. number expected (10,000,000) and saying that it was time to raise the threshold. Instead, I changed the code to look at only the first 10,000,000 proteins, with the assumption that that had better be enough for estimating the distribution of amino acid properties
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 72, context: html, text, full: html, text
    Updates to UCSC Genes: (1) removed code to rebuild tables used by the proteome browser, now that the proteome browser is no longer used for hg19 (2) updated the code to parse the kegg tables, to adapt to what appears to be a change in format on kegg's side
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html
  • lines changed 3, context: html, text, full: html, text
    (1) Removed an inaccurate sentence from the Unc/Bsu Prot track description page. (2) In the 101005.txt protein database script, added a shell variable to represent the base of the kent source tree. (3) In pbCalDistGlobal, there was an errAbort condition indicating that the number of proteins exceeded the max. number expected (10,000,000) and saying that it was time to raise the threshold. Instead, I changed the code to look at only the first 10,000,000 proteins, with the assumption that that had better be enough for estimating the distribution of amino acid properties
  • lines changed 5, context: html, text, full: html, text
    Addressing some QA comments on this track details page
  • lines changed 8, context: html, text, full: html, text
    Reordered the extra bed6+ fields to make them consistent with the order in which they appear in the schema
  • lines changed 105, context: html, text, full: html, text
    Cleaning up a conflicted merge
  • lines changed 11, context: html, text, full: html, text
    Set the useScore .ra file variable to render the uncBsuProt track items in grayscale, according to the score. Updated the track description page to reflect this change
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.new.ra
  • lines changed 1, context: html, text, full: html, text
    Set the useScore .ra file variable to render the uncBsuProt track items in grayscale, according to the score. Updated the track description page to reflect this change
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra
  • lines changed 1, context: html, text, full: html, text
    Set the useScore .ra file variable to render the uncBsuProt track items in grayscale, according to the score. Updated the track description page to reflect this change
• src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c
  • lines changed 4, context: html, text, full: html, text
    (1) Removed an inaccurate sentence from the Unc/Bsu Prot track description page. (2) In the 101005.txt protein database script, added a shell variable to represent the base of the kent source tree. (3) In pbCalDistGlobal, there was an errAbort condition indicating that the number of proteins exceeded the max. number expected (10,000,000) and saying that it was time to raise the threshold. Instead, I changed the code to look at only the first 10,000,000 proteins, with the assumption that that had better be enough for estimating the distribution of amino acid properties