File Changes for max

v298_preview2 to v298_base (2014-03-31 to 2014-04-07) v298

• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 2, context: html, text, full: html, text
    changing hgLiftOver strategy in the browserbox: downloading liftoverfiles to local disk instead of streaming them through http, refs #11957
    and refs #12717
    
• src/hg/hgVai/hgVai.c
  • lines changed 3, context: html, text, full: html, text
    Fixing hgVai again for gbib, refs #11957 and refs #12717. One problemwas that show tables cannot fail over. Probably need to libify
    one day as a sqlShowTables() function. Another problem are the nib
    directories in hg18. Working towards replacing all nib directories with their
    twoBit versions via a hg.conf statement.
    
  • lines changed 7, context: html, text, full: html, text
    Libifying yesterday's commit and applying another patch to hgVai to makeit work in the browserbox, refs #11957 and #12717
    
• src/hg/hgc/bamClick.c
  • lines changed 2, context: html, text, full: html, text
    making hgc bam clicks gbib-ready, refs #11957 and refs #12717
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 3, context: html, text, full: html, text
    changes after code review, refs #12998
• src/hg/inc/hdb.h
  • lines changed 9, context: html, text, full: html, text
    changing hgLiftOver strategy in the browserbox: downloading liftoverfiles to local disk instead of streaming them through http, refs #11957
    and refs #12717
    
• src/hg/inc/jksql.h
  • lines changed 3, context: html, text, full: html, text
    Fixing hgVai again for gbib, refs #11957 and refs #12717. One problemwas that show tables cannot fail over. Probably need to libify
    one day as a sqlShowTables() function. Another problem are the nib
    directories in hg18. Working towards replacing all nib directories with their
    twoBit versions via a hg.conf statement.
    
  • lines changed 4, context: html, text, full: html, text
    Libifying yesterday's commit and applying another patch to hgVai to makeit work in the browserbox, refs #11957 and #12717
    
• src/hg/lib/hdb.c
  • lines changed 61, context: html, text, full: html, text
    changing hgLiftOver strategy in the browserbox: downloading liftoverfiles to local disk instead of streaming them through http, refs #11957
    and refs #12717
    
  • lines changed 13, context: html, text, full: html, text
    Fixing hgVai again for gbib, refs #11957 and refs #12717. One problemwas that show tables cannot fail over. Probably need to libify
    one day as a sqlShowTables() function. Another problem are the nib
    directories in hg18. Working towards replacing all nib directories with their
    twoBit versions via a hg.conf statement.
    
  • lines changed 2, context: html, text, full: html, text
    oops forgot to check for null pointer in last commit.
  • lines changed 1, context: html, text, full: html, text
    further support to remove .nib access via an hg.conf option. refs #11957
• src/hg/lib/jksql.c
  • lines changed 7, context: html, text, full: html, text
    Fixing hgVai again for gbib, refs #11957 and refs #12717. One problemwas that show tables cannot fail over. Probably need to libify
    one day as a sqlShowTables() function. Another problem are the nib
    directories in hg18. Working towards replacing all nib directories with their
    twoBit versions via a hg.conf statement.
    
  • lines changed 24, context: html, text, full: html, text
    Libifying yesterday's commit and applying another patch to hgVai to makeit work in the browserbox, refs #11957 and #12717
    
  • lines changed 2, context: html, text, full: html, text
    fixing a mysqlinj bug in last commit
  • lines changed 37, context: html, text, full: html, text
    when using a failover connection but no table cache, merge the tablelists from both the failover connection and the main connection.
    Otherwise only local tracks show up. for this, extracting
    old code into a new function and calling it twice. (NB: This code change
    is very hard to see in the diff algorithm we use in the git reports.
    The "patience" algorithm is a lot better: git diff --patience jksql.c)
    
• src/hg/lib/liftOver.c
  • lines changed 1, context: html, text, full: html, text
    changing hgLiftOver strategy in the browserbox: downloading liftoverfiles to local disk instead of streaming them through http, refs #11957
    and refs #12717
    
• src/hg/utils/makeTableList/makeTableList.c
  • lines changed 1, context: html, text, full: html, text
    making makeTableList work for Jorge who has no hg.conf and his hgcentralhave no user or sessionDb tables. refs #11957
    
• src/lib/paraFetch.c
  • lines changed 1, context: html, text, full: html, text
    fixing an error message
• src/makefile
  • lines changed 18, context: html, text, full: html, text
    adding a top level target for htdocs+js+css, refs #12717 note 27
• src/product/ex.hg.conf
  • lines changed 4, context: html, text, full: html, text
    hg.conf doc change after code review, refs #12998
  • lines changed 4, context: html, text, full: html, text
    Fixing hgVai again for gbib, refs #11957 and refs #12717. One problemwas that show tables cannot fail over. Probably need to libify
    one day as a sqlShowTables() function. Another problem are the nib
    directories in hg18. Working towards replacing all nib directories with their
    twoBit versions via a hg.conf statement.