File Changes for galt

v278_base to v279_preview (2013-01-22 to 2013-01-29) v279

• src/blat/version.doc
  • lines changed 1, context: html, text, full: html, text
    Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general.
  • lines changed 1, context: html, text, full: html, text
    Revert "Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general."
    This reverts commit ef98cc65cd9626157087f5ad3dd6eac5012c50d8.
    
    Turns out that on some rare cases the relative paths were useful.
    Instead will add a message to gfServer explaining better how the
    paths in the filenames given will be used.
    
• src/gfServer/gfServer.c
  • lines changed 8, context: html, text, full: html, text
    Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general.
  • lines changed 8, context: html, text, full: html, text
    Revert "Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general."
    This reverts commit ef98cc65cd9626157087f5ad3dd6eac5012c50d8.
    
    Turns out that on some rare cases the relative paths were useful.
    Instead will add a message to gfServer explaining better how the
    paths in the filenames given will be used.
    
  • lines changed 11, context: html, text, full: html, text
    Added detailed description of how paths are handled between gfServer commandline and the various clients that use gfServer.
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    set udc cache location early before cart and doMiddle if possible. Restoring saved sessions with bigDataUrl custom tracks was leaking to /tmp/udcCache instead of correct CGI location under trash.
• src/hg/hgTracks/mainMain.c
  • lines changed 2, context: html, text, full: html, text
    set udc cache location early before cart and doMiddle if possible. Restoring saved sessions with bigDataUrl custom tracks was leaking to /tmp/udcCache instead of correct CGI location under trash.
  • lines changed 1, context: html, text, full: html, text
    removing unneeded include
• src/hg/hgTracks/renderMain.c
  • lines changed 1, context: html, text, full: html, text
    set udc cache location early before cart and doMiddle if possible. Restoring saved sessions with bigDataUrl custom tracks was leaking to /tmp/udcCache instead of correct CGI location under trash.
• src/hg/lib/customFactory.c
  • lines changed 5, context: html, text, full: html, text
    Tricky cart session handling calls custom track parser early, so need to set the udc cache dir here in a CGI-independent way.
• src/hg/lib/geoMirror.c
  • lines changed 9, context: html, text, full: html, text
    better documentation of geoSuffix and testing
• src/inc/common.h
  • lines changed 3, context: html, text, full: html, text
    Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general.
  • lines changed 3, context: html, text, full: html, text
    Revert "Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general."
    This reverts commit ef98cc65cd9626157087f5ad3dd6eac5012c50d8.
    
    Turns out that on some rare cases the relative paths were useful.
    Instead will add a message to gfServer explaining better how the
    paths in the filenames given will be used.
    
• src/inc/genoFind.h
  • lines changed 1, context: html, text, full: html, text
    Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general.
  • lines changed 1, context: html, text, full: html, text
    Revert "Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general."
    This reverts commit ef98cc65cd9626157087f5ad3dd6eac5012c50d8.
    
    Turns out that on some rare cases the relative paths were useful.
    Instead will add a message to gfServer explaining better how the
    paths in the filenames given will be used.
    
• src/jkOwnLib/genoFind.c
  • lines changed 7, context: html, text, full: html, text
    Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general.
  • lines changed 7, context: html, text, full: html, text
    Revert "Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general."
    This reverts commit ef98cc65cd9626157087f5ad3dd6eac5012c50d8.
    
    Turns out that on some rare cases the relative paths were useful.
    Instead will add a message to gfServer explaining better how the
    paths in the filenames given will be used.
    
• src/lib/common.c
  • lines changed 10, context: html, text, full: html, text
    Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general.
  • lines changed 10, context: html, text, full: html, text
    Revert "Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general."
    This reverts commit ef98cc65cd9626157087f5ad3dd6eac5012c50d8.
    
    Turns out that on some rare cases the relative paths were useful.
    Instead will add a message to gfServer explaining better how the
    paths in the filenames given will be used.
    
• src/webBlat/install.txt
  • lines changed 5, context: html, text, full: html, text
    Fixed incorrect and misleading config lines in documentation for webBlat.